[gmx-users] Need small well known QM/MM example

[Ake Sandgren]

Hi!

I need a small QM/MM gromacs input data with a well known result (and
preferably the output too) to compare to the gromacs/gamess-uk setup i'm
testing.

Does anyone have something i can use?

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

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RE: [gmx-users] Software inconsistency error: Not enough water

[Berk Hess]

Hi,

This error message in incorrect, it is probably not a software inconsistency.
Looking at the code, it seems the problem is that the topology file
you provided does not have enough SOL molecules in the [molecules ] section.
I'll fix this error message for the next release.

Berk

From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 12:48:53 +0530
To: gmx-users@gromacs.org
Subject: [gmx-users] Software inconsistency error: Not enough water

Hello gmxusers !!
I am simulating a protein and it  is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too 
works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) 
file.


Error:

$ genion -s em.tpr -o ion.pdb -p topol.top -np 48 
WARNING: turning of free energy, will use lambda=0   
Reading file em.tpr, VERSION 4.0.7 (single precision)
Using a coulomb cut-off of 0.9 nm


Will try to add 48 Na ions and 0 Cl ions.
Select a continuous group of solvent molecules   
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 70056 elements   


Group 1 ( Protein) has 10214 elements   
Group 2 (   Protein-H) has  5107 elements   
Group 3 ( C-alpha) has   623 elements   


Group 4 (Backbone) has  1869 elements   
Group 5 (   MainChain) has  2488 elements   
Group 6 (MainChain+Cb) has  3083 elements   


Group 7 ( MainChain+H) has  3099 elements   
Group 8 (   SideChain) has  7115 elements   
Group 9 ( SideChain-H) has  2619 elements
Group10 ( Prot-Masses) has 10214 elements


Group11 ( Non-Protein) has 59842 elements
Group12 ( ATP) has43 elements
Group13 ( SOL) has 59799 elements
Group14 (   Other) has 59842 elements
Select a group: 13
Selected 13: 'SOL'


Number of (3-atomic) solvent molecules: 19933

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.1#

---
Program genion, VERSION 4.0.7


Source code file: gmx_genion.c, line: 269

Software inconsistency error:
Not enough water
---

Though my system has sufficient amount of water (19933) molecules. Can not 
understand the error. Any information would be useful.




Chadan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
  
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RE: [gmx-users] Software inconsistency error: Not enough water

[Berk Hess]

Hi,

Could it be that you have multiple SOL entries in the [ molecules ] section,
a first one for the crystal waters, with less than 48 molecules and then
one with the rest of the waters?
In that case genion should subtract the water molecules from the last SOL entry,
the current version takes the first SOL entry.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Software inconsistency error: Not enough water
Date: Thu, 11 Feb 2010 11:08:38 +0100








Hi,

This error message in incorrect, it is probably not a software inconsistency.
Looking at the code, it seems the problem is that the topology file
you provided does not have enough SOL molecules in the [molecules ] section.
I'll fix this error message for the next release.

Berk

From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 12:48:53 +0530
To: gmx-users@gromacs.org
Subject: [gmx-users] Software inconsistency error: Not enough water

Hello gmxusers !!
I am simulating a protein and it  is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too 
works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) 
file.


Error:

$ genion -s em.tpr -o ion.pdb -p topol.top -np 48 
WARNING: turning of free energy, will use lambda=0   
Reading file em.tpr, VERSION 4.0.7 (single precision)
Using a coulomb cut-off of 0.9 nm


Will try to add 48 Na ions and 0 Cl ions.
Select a continuous group of solvent molecules   
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 70056 elements   


Group 1 ( Protein) has 10214 elements   
Group 2 (   Protein-H) has  5107 elements   
Group 3 ( C-alpha) has   623 elements   


Group 4 (Backbone) has  1869 elements   
Group 5 (   MainChain) has  2488 elements   
Group 6 (MainChain+Cb) has  3083 elements   


Group 7 ( MainChain+H) has  3099 elements   
Group 8 (   SideChain) has  7115 elements   
Group 9 ( SideChain-H) has  2619 elements
Group10 ( Prot-Masses) has 10214 elements


Group11 ( Non-Protein) has 59842 elements
Group12 ( ATP) has43 elements
Group13 ( SOL) has 59799 elements
Group14 (   Other) has 59842 elements
Select a group: 13
Selected 13: 'SOL'


Number of (3-atomic) solvent molecules: 19933

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.1#

---
Program genion, VERSION 4.0.7


Source code file: gmx_genion.c, line: 269

Software inconsistency error:
Not enough water
---

Though my system has sufficient amount of water (19933) molecules. Can not 
understand the error. Any information would be useful.




Chadan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
  
Express yourself instantly with MSN Messenger! MSN Messenger
  
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[gmx-users] Range checking error

[011013021-Jyotsna]

Dear all,

I am simulating a protein along with a ligand molecule. 
The ligand molecule is modeled as per the literature. The 
ligand molecule consists of FE and S alone and in addition 
to that it is covalently bonded with the enzyme's cys 
residue. So I have modeled my ligand FE4S4 with SG and CB 
atoms of cystine. I have included only bonded terms in my 
forcefield for my ligand (since I do not know other terms 
like angle and dihedral angles force constants etc) and 
the article does not mention these.


Now the problem is, when I try to run energy minimization 
, I encounter  "Range checking error:" and the detailed 
error is pasted below. So I suspect this error is due to 
inadequate force field data like angles and dihedrals. Or 
is it caused by some other factor?.But one thing I am sure 
of is , when I simulate my system without the ligand, the 
error disappears. I am unable to find any answer to this 
query in the forum.


Kindly extend your help this time as you always do.


#
Steepest Descents:
   Tolerance (Fmax)   =  2.0e+02
   Number of steps= 5000
Warning: 1-4 interaction between 2446 and 2468 at distance 
6.079 which is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp 
file

or with user tables increase the table size
Step=0, Dmax= 1.0e-02 nm, Epot=  nan Fmax= 
1.71540e+115, atom= 2452

---
Program mdrun_d, VERSION 4.0
Source code file: nsgrid.c, line: 357

Range checking error:
Explanation: During neighborsearching, we assign each 
particle to a grid
based on its coordinates. If your system contains 
collisions or parameter
errors that give particles very high velocities you might 
end up with some
coordinates being +-Infinity or NaN (not-a-number). 
Obviously, we cannot
put these on a grid, so this is usually where we detect 
those errors.
Make sure your system is properly energy-minimized and 
that the potential

energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been 
within [ 0 .. 4096 ]


#

Thank You
Jyotsna














On Wed, 03 Feb 2010 22:42:09 +1100
 Mark Abraham  wrote:
*This message was transferred with a trial version of 
CommuniGate(r) Pro*



- Original Message -
From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu>
Date: Wednesday, February 3, 2010 21:48
Subject: Re: [gmx-users] H2 topology
To: Discussion list for GROMACS users 





Dear David,

Thanks for your reply.  From your reply, I get the 
impression that the bond length of my hydrogen molecule 
gets 
adjusted duing minimization of the whole system ( 
protien+water+ 
inserted hydrogen molecule). But the issue impending is 
the 
insertion of the hydrogen molecule itself into the 
protein+water 
box created in previous step. For insertion/addition of 
hydrogen 
molecules I used the command:


genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top 
–ci 
h2.gro –nmol 100


What about a two-stage process? Do genbox -ci h2.gro 
-nmol 100 when there's no water, and then solvate 
*afterwards*.


Or, generate solvent, and get a list of 100 random 
numbers in the right range, manually delete those water 
molecules to create interstices, update your [molecules] 
section, then use genconf -ci and equilibrate carefully 
to fix the density.


Or, generate solvent for a box somewhat smaller than the 
one you want, use editconf -scale to scale the 
coordinates up to create interstices, use genconf -ci and 
then minimize really gently to fix all the bond lengths, 
and equilibrate carefully to fix the density.


Mark

 It reports to me the inability to add any of the 
hydrogen 
molecules, ie it adds 0 molecules out of 100 requested.

###error
Reading molecule configuration
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
Containing 3 atoms in 1 residue
Initialising van der waals distances...
Try 999
Added 0 molecules (out of 100 requested) of H2
Writing generated configuration to 2frv.solv.gro

Back Off! I just backed up 2frv.solv.gro to 
./#2frv.solv.gro.1#

PERIPLASMIC HYDROGENASE; PERIPLASMIC HYDROGENASE

Output configuration contains 8340 atoms in 977 residues
Volume : 1299.08 (nm^3)
Density : 143.043 (g/l)
Number of SOL molecules: 186

Processing topology
Removing line #40 'SOL 39308' from topology file 
(2frv.top)

error end###
How do i rectify this problem?
 I suspect the problem is due to the bond length of the 
hydrogen molecule that I created with 1.66A distance ( 
as 
described in my previous post) and the fact that the gap 
between 
the solvent molecules (in my case , water) is not big 
enough to 
accomodate the H2 molecules(as I h

Re: [gmx-users] Range checking error

[Justin A. Lemkul]

011013021-Jyotsna wrote:


Dear all,

I am simulating a protein along with a ligand molecule. The ligand 
molecule is modeled as per the literature. The ligand molecule consists 
of FE and S alone and in addition to that it is covalently bonded with 
the enzyme's cys residue. So I have modeled my ligand FE4S4 with SG and 
CB atoms of cystine. I have included only bonded terms in my forcefield 
for my ligand (since I do not know other terms like angle and dihedral 
angles force constants etc) and the article does not mention these.


Now the problem is, when I try to run energy minimization , I encounter  
"Range checking error:" and the detailed error is pasted below. So I 
suspect this error is due to inadequate force field data like angles and 
dihedrals. Or is it caused by some other factor?.But one thing I am sure 


More likely the underlying physics is unreasonable.  See here:

http://www.gromacs.org/Documentation/Errors#Range_Checking_error

of is , when I simulate my system without the ligand, the error 
disappears. I am unable to find any answer to this query in the forum.


Kindly extend your help this time as you always do.


#
Steepest Descents:
   Tolerance (Fmax)   =  2.0e+02
   Number of steps= 5000
Warning: 1-4 interaction between 2446 and 2468 at distance 6.079 which 
is larger than the 1-4 table size 2.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
Step=0, Dmax= 1.0e-02 nm, Epot=  nan Fmax= 1.71540e+115, 
atom= 2452


You should have seen these errors in the list archive if you did a search.  Your 
system is clearly blowing up (see link above).  Your Fmax is essentially 
infinite, which is usually due to extreme atomic overlap, which should be clear 
in the input structure.  Otherwise, mdrun is giving you clues about atoms 2446 
and 2468 - start investigating there.



---
Program mdrun_d, VERSION 4.0
Source code file: nsgrid.c, line: 357



I would also encourage you to upgrade to the latest version (4.0.7); it will not 
fix your problem, but there have certainly been some important bug fixes related 
to stability and usability that will make your life easier :)


-Justin


Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 4096 ]

# 



Thank You
Jyotsna














On Wed, 03 Feb 2010 22:42:09 +1100
 Mark Abraham  wrote:

*This message was transferred with a trial version of CommuniGate(r) Pro*


- Original Message -
From: 011013021-Jyotsna <011013...@bioinfo.sastra.edu>
Date: Wednesday, February 3, 2010 21:48
Subject: Re: [gmx-users] H2 topology
To: Discussion list for GROMACS users 



Dear David,

Thanks for your reply.  From your reply, I get the impression that 
the bond length of my hydrogen molecule gets adjusted duing 
minimization of the whole system ( protien+water+ inserted hydrogen 
molecule). But the issue impending is the insertion of the hydrogen 
molecule itself into the protein+water box created in previous step. 
For insertion/addition of hydrogen molecules I used the command:


genbox_d -cp 2frv.conf.gro -o 2frv.solv.gro -p 2frv.top –ci h2.gro 
–nmol 100


What about a two-stage process? Do genbox -ci h2.gro -nmol 100 when 
there's no water, and then solvate *afterwards*.


Or, generate solvent, and get a list of 100 random numbers in the 
right range, manually delete those water molecules to create 
interstices, update your [molecules] section, then use genconf -ci and 
equilibrate carefully to fix the density.


Or, generate solvent for a box somewhat smaller than the one you want, 
use editconf -scale to scale the coordinates up to create interstices, 
use genconf -ci and then minimize really gently to fix all the bond 
lengths, and equilibrate carefully to fix the density.


Mark

 It reports to me the inability to add any of the hydrogen molecules, 
ie it adds 0 molecules out of 100 requested.

###error
Reading molecule configuration
Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
Containing 3 atoms in 1 residue
Initialising van der waals distances...
Try 999
Added 0 molecules (out of 100 requested) of H2
Writing ge

Re: [gmx-users] Software inconsistency error: Not enough water

[Chandan Choudhury]

Thanks berk.
By the way, if I dont give -p topol.top as input to genion, then genion
executes. In this case, I manually edit the topology file and add the ion
information.
 [ molecules ]
; Compound#mols
Protein_A   1
Protein_B   1
Protein_C   1
Protein_D   1
Protein_E   1
SOL32
SOL46
SOL 3
SOL13
SOL 19791
Na 48

This is my part of topology after adding ions (Na). In the previous case of
genion was only considering first SOL information, which has only 32
molecules.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  wrote:

>  Hi,
>
> This error message in incorrect, it is probably not a software
> inconsistency.
> Looking at the code, it seems the problem is that the topology file
> you provided does not have enough SOL molecules in the [molecules ]
> section.
> I'll fix this error message for the next release.
>
> Berk
>
> --
> From: iitd...@gmail.com
> Date: Thu, 11 Feb 2010 12:48:53 +0530
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Software inconsistency error: Not enough water
>
>
> Hello gmxusers !!
> I am simulating a protein and it  is bound to ATP.
> Simulation of protein alone (without) works fine. Solely ATP simulation too
> works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb)
> file.
> Error:
>
>
> $ genion -s em.tpr -o ion.pdb -p topol.top -np 48
> WARNING: turning of free energy, will use lambda=0
> Reading file em.tpr, VERSION 4.0.7 (single precision)
> Using a coulomb cut-off of 0.9 nm
> Will try to add 48 Na ions and 0 Cl ions.
> Select a continuous group of solvent molecules
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Group 0 (  System) has 70056 elements
> Group 1 ( Protein) has 10214 elements
> Group 2 (   Protein-H) has  5107 elements
> Group 3 ( C-alpha) has   623 elements
> Group 4 (Backbone) has  1869 elements
> Group 5 (   MainChain) has  2488 elements
> Group 6 (MainChain+Cb) has  3083 elements
> Group 7 ( MainChain+H) has  3099 elements
> Group 8 (   SideChain) has  7115 elements
> Group 9 ( SideChain-H) has  2619 elements
> Group10 ( Prot-Masses) has 10214 elements
> Group11 ( Non-Protein) has 59842 elements
> Group12 ( ATP) has43 elements
> Group13 ( SOL) has 59799 elements
> Group14 (   Other) has 59842 elements
> Select a group: 13
> Selected 13: 'SOL'
> Number of (3-atomic) solvent molecules: 19933
>
> Processing topology
>
> Back Off! I just backed up temp.top to ./#temp.top.1#
>
> ---
> Program genion, VERSION 4.0.7
> Source code file: gmx_genion.c, line: 269
>
> Software inconsistency error:
> Not enough water
> ---
>
> Though my system has sufficient amount of water (19933) molecules. Can not
> understand the error. Any information would be useful.
>
>
> Chadan
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
> --
> Express yourself instantly with MSN Messenger! MSN 
> Messenger
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Please search the archive at http://www.gromacs.org/search before posting!
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RE: [gmx-users] Software inconsistency error: Not enough water

[Berk Hess]

Hi,

genion in future Gromacs versions will only use the last SOL block
and give a proper error message when there is not enough water.

Berk

From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users@gromacs.org

Thanks berk.
By the way, if I dont give -p topol.top as input to genion, then genion 
executes. In this case, I manually edit the topology file and add the ion 
information.
 [ molecules ]
; Compound#mols


Protein_A   1
Protein_B   1
Protein_C   1
Protein_D   1
Protein_E   1
SOL32
SOL46
SOL 3
SOL13


SOL 19791
Na 48

This is my part of topology after adding ions (Na). In the previous case of 
genion was only considering first SOL information, which has only 32 molecules.

Chandan  




--
Chandan kumar Choudhury
NCL, Pune
INDIA



On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  wrote:







Hi,

This error message in incorrect, it is probably not a software inconsistency.
Looking at the code, it seems the problem is that the topology file
you provided does not have enough SOL molecules in the [molecules ] section.


I'll fix this error message for the next release.

Berk

From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 12:48:53 +0530
To: gmx-users@gromacs.org


Subject: [gmx-users] Software inconsistency error: Not enough water

Hello gmxusers !!
I am simulating a protein and it  is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too 
works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb) 
file.




Error:

$ genion -s em.tpr -o ion.pdb -p topol.top -np 48 
WARNING: turning of free energy, will use lambda=0   
Reading file em.tpr, VERSION 4.0.7 (single precision)
Using a coulomb cut-off of 0.9 nm




Will try to add 48 Na ions and 0 Cl ions.
Select a continuous group of solvent molecules   
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 70056 elements   




Group 1 ( Protein) has 10214 elements   
Group 2 (   Protein-H) has  5107 elements   
Group 3 ( C-alpha) has   623 elements   




Group 4 (Backbone) has  1869 elements   
Group 5 (   MainChain) has  2488 elements   
Group 6 (MainChain+Cb) has  3083 elements   




Group 7 ( MainChain+H) has  3099 elements   
Group 8 (   SideChain) has  7115 elements   
Group 9 ( SideChain-H) has  2619 elements
Group10 ( Prot-Masses) has 10214 elements




Group11 ( Non-Protein) has 59842 elements
Group12 ( ATP) has43 elements
Group13 ( SOL) has 59799 elements
Group14 (   Other) has 59842 elements
Select a group: 13
Selected 13: 'SOL'




Number of (3-atomic) solvent molecules: 19933

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.1#

---
Program genion, VERSION 4.0.7




Source code file: gmx_genion.c, line: 269

Software inconsistency error:
Not enough water
---

Though my system has sufficient amount of water (19933) molecules. Can not 
understand the error. Any information would be useful.






Chadan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
  
Express yourself instantly with MSN Messenger! MSN Messenger



--

gmx-users mailing listgmx-users@gromacs.org

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Please search the archive at http://www.gromacs.org/search before posting!

Please don't post (un)subscribe requests to the list. Use the

www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

  
_
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Re: [gmx-users] Software inconsistency error: Not enough water

[Erik Marklund]

Hi,

Is it desirable that genion only considers a single SOL block? Why not 
use them all if there are many?


Regards,

Erik

Berk Hess skrev:

Hi,

genion in future Gromacs versions will only use the last SOL block
and give a proper error message when there is not enough water.

Berk


From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users@gromacs.org


Thanks berk.
By the way, if I dont give -p topol.top as input to genion, then 
genion executes. In this case, I manually edit the topology file and 
add the ion information.

 [ molecules ]
; Compound#mols
Protein_A   1
Protein_B   1
Protein_C   1
Protein_D   1
Protein_E   1
SOL32
SOL46
SOL 3
SOL13
SOL 19791
Na 48

This is my part of topology after adding ions (Na). In the previous 
case of genion was only considering first SOL information, which has 
only 32 molecules.


Chandan 



--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess > wrote:


Hi,

This error message in incorrect, it is probably not a software
inconsistency.
Looking at the code, it seems the problem is that the topology file
you provided does not have enough SOL molecules in the [molecules
] section.
I'll fix this error message for the next release.

Berk


From: iitd...@gmail.com 
Date: Thu, 11 Feb 2010 12:48:53 +0530
To: gmx-users@gromacs.org 
Subject: [gmx-users] Software inconsistency error: Not enough water


Hello gmxusers !!
I am simulating a protein and it  is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP
simulation too works. But the problem arises on adding ions to the
protein + ATP (1QHH.pdb) file.
Error:


$ genion -s em.tpr -o ion.pdb -p topol.top -np 48
WARNING: turning of free energy, will use lambda=0  
Reading file em.tpr, VERSION 4.0.7 (single precision)   
Using a coulomb cut-off of 0.9 nm   
Will try to add 48 Na ions and 0 Cl ions.   
Select a continuous group of solvent molecules  
Opening library file

/usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 (  System) has 70056
elements  
Group 1 ( Protein) has 10214
elements  
Group 2 (   Protein-H) has  5107
elements  
Group 3 ( C-alpha) has   623
elements  
Group 4 (Backbone) has  1869
elements  
Group 5 (   MainChain) has  2488
elements  
Group 6 (MainChain+Cb) has  3083
elements  
Group 7 ( MainChain+H) has  3099
elements  
Group 8 (   SideChain) has  7115
elements  
Group 9 ( SideChain-H) has  2619 elements

Group10 ( Prot-Masses) has 10214 elements
Group11 ( Non-Protein) has 59842 elements
Group12 ( ATP) has43 elements
Group13 ( SOL) has 59799 elements
Group14 (   Other) has 59842 elements
Select a group: 13
Selected 13: 'SOL'
Number of (3-atomic) solvent molecules: 19933

Processing topology

Back Off! I just backed up temp.top to ./#temp.top.1#

---
Program genion, VERSION 4.0.7
Source code file: gmx_genion.c, line: 269

Software inconsistency error:
Not enough water
---

Though my system has sufficient amount of water (19933) molecules.
Can not understand the error. Any information would be useful.


Chadan
--
Chandan kumar Choudhury
NCL, Pune
INDIA


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RE: [gmx-users] Software inconsistency error: Not enough water

[Berk Hess]

Hi,

We are getting to much detail now.
In principle yes, but since you get a clear error message now, I wouldn't worry 
about this.
The chance that the last water block is willingly smaller than the number of 
ions is about zero.

Berk

> Date: Thu, 11 Feb 2010 13:34:59 +0100
> From: er...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> 
> Hi,
> 
> Is it desirable that genion only considers a single SOL block? Why not 
> use them all if there are many?
> 
> Regards,
> 
> Erik
> 
> Berk Hess skrev:
> > Hi,
> >
> > genion in future Gromacs versions will only use the last SOL block
> > and give a proper error message when there is not enough water.
> >
> > Berk
> >
> > 
> > From: iitd...@gmail.com
> > Date: Thu, 11 Feb 2010 16:45:06 +0530
> > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> > To: gmx-users@gromacs.org
> >
> >
> > Thanks berk.
> > By the way, if I dont give -p topol.top as input to genion, then 
> > genion executes. In this case, I manually edit the topology file and 
> > add the ion information.
> >  [ molecules ]
> > ; Compound#mols
> > Protein_A   1
> > Protein_B   1
> > Protein_C   1
> > Protein_D   1
> > Protein_E   1
> > SOL32
> > SOL46
> > SOL 3
> > SOL13
> > SOL 19791
> > Na 48
> >
> > This is my part of topology after adding ions (Na). In the previous 
> > case of genion was only considering first SOL information, which has 
> > only 32 molecules.
> >
> > Chandan 
> >
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> >
> >
> > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  > > wrote:
> >
> > Hi,
> >
> > This error message in incorrect, it is probably not a software
> > inconsistency.
> > Looking at the code, it seems the problem is that the topology file
> > you provided does not have enough SOL molecules in the [molecules
> > ] section.
> > I'll fix this error message for the next release.
> >
> > Berk
> >
> > 
> > From: iitd...@gmail.com 
> > Date: Thu, 11 Feb 2010 12:48:53 +0530
> > To: gmx-users@gromacs.org 
> > Subject: [gmx-users] Software inconsistency error: Not enough water
> >
> >
> > Hello gmxusers !!
> > I am simulating a protein and it  is bound to ATP.
> > Simulation of protein alone (without) works fine. Solely ATP
> > simulation too works. But the problem arises on adding ions to the
> > protein + ATP (1QHH.pdb) file.
> > Error:
> >
> >
> > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48
> > WARNING: turning of free energy, will use lambda=0  
> > Reading file em.tpr, VERSION 4.0.7 (single precision)   
> > Using a coulomb cut-off of 0.9 nm   
> > Will try to add 48 Na ions and 0 Cl ions.   
> > Select a continuous group of solvent molecules  
> > Opening library file
> > /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> > Group 0 (  System) has 70056
> > elements  
> > Group 1 ( Protein) has 10214
> > elements  
> > Group 2 (   Protein-H) has  5107
> > elements  
> > Group 3 ( C-alpha) has   623
> > elements  
> > Group 4 (Backbone) has  1869
> > elements  
> > Group 5 (   MainChain) has  2488
> > elements  
> > Group 6 (MainChain+Cb) has  3083
> > elements  
> > Group 7 ( MainChain+H) has  3099
> > elements  
> > Group 8 (   SideChain) has  7115
> > elements  
> > Group 9 ( SideChain-H) has  2619 elements
> > Group10 ( Prot-Masses) has 10214 elements
> > Group11 ( Non-Protein) has 59842 elements
> > Group12 ( ATP) has43 elements
> > Group13 ( SOL) has 59799 elements
> > Group14 (   Other) has 59842 elements
> > Select a group: 13
> > Selected 13: 'SOL'
> > Number of (3-atomic) solvent molecules: 19933
> >
> > Processing topology
> >
> > Back Off! I just backed up temp.top to ./#temp.top.1#
> >
> > ---
> > Program genion, VERSION 4.0.7
> > Source code file: gmx_genion.c, line: 269
> >
> > Software inconsistency error:
> > Not enough water
> > ---
> >
> > Though my system has sufficient amount o

Re: [gmx-users] Software inconsistency error: Not enough water

[Thomas Piggot]

Plus I suppose that if you have kept the crystal waters you would not 
want them to be replaced by genion.


Tom

Berk Hess wrote:

Hi,

We are getting to much detail now.
In principle yes, but since you get a clear error message now, I 
wouldn't worry about this.
The chance that the last water block is willingly smaller than the 
number of ions is about zero.


Berk

 > Date: Thu, 11 Feb 2010 13:34:59 +0100
 > From: er...@xray.bmc.uu.se
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
 >
 > Hi,
 >
 > Is it desirable that genion only considers a single SOL block? Why not
 > use them all if there are many?
 >
 > Regards,
 >
 > Erik
 >
 > Berk Hess skrev:
 > > Hi,
 > >
 > > genion in future Gromacs versions will only use the last SOL block
 > > and give a proper error message when there is not enough water.
 > >
 > > Berk
 > >
 > > 


 > > From: iitd...@gmail.com
 > > Date: Thu, 11 Feb 2010 16:45:06 +0530
 > > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
 > > To: gmx-users@gromacs.org
 > >
 > >
 > > Thanks berk.
 > > By the way, if I dont give -p topol.top as input to genion, then
 > > genion executes. In this case, I manually edit the topology file and
 > > add the ion information.
 > > [ molecules ]
 > > ; Compound #mols
 > > Protein_A 1
 > > Protein_B 1
 > > Protein_C 1
 > > Protein_D 1
 > > Protein_E 1
 > > SOL 32
 > > SOL 46
 > > SOL 3
 > > SOL 13
 > > SOL 19791
 > > Na 48
 > >
 > > This is my part of topology after adding ions (Na). In the previous
 > > case of genion was only considering first SOL information, which has
 > > only 32 molecules.
 > >
 > > Chandan
 > >
 > >
 > > --
 > > Chandan kumar Choudhury
 > > NCL, Pune
 > > INDIA
 > >
 > >
 > > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  > > wrote:
 > >
 > > Hi,
 > >
 > > This error message in incorrect, it is probably not a software
 > > inconsistency.
 > > Looking at the code, it seems the problem is that the topology file
 > > you provided does not have enough SOL molecules in the [molecules
 > > ] section.
 > > I'll fix this error message for the next release.
 > >
 > > Berk
 > >
 > > 


 > > From: iitd...@gmail.com 
 > > Date: Thu, 11 Feb 2010 12:48:53 +0530
 > > To: gmx-users@gromacs.org 
 > > Subject: [gmx-users] Software inconsistency error: Not enough water
 > >
 > >
 > > Hello gmxusers !!
 > > I am simulating a protein and it is bound to ATP.
 > > Simulation of protein alone (without) works fine. Solely ATP
 > > simulation too works. But the problem arises on adding ions to the
 > > protein + ATP (1QHH.pdb) file.
 > > Error:
 > >
 > >
 > > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48
 > > WARNING: turning of free energy, will use lambda=0
 > > Reading file em.tpr, VERSION 4.0.7 (single precision)
 > > Using a coulomb cut-off of 0.9 nm
 > > Will try to add 48 Na ions and 0 Cl ions.
 > > Select a continuous group of solvent molecules
 > > Opening library file
 > > /usr/local/gromacs/share/gromacs/top/aminoacids.dat
 > > Group 0 ( System) has 70056
 > > elements
 > > Group 1 ( Protein) has 10214
 > > elements
 > > Group 2 ( Protein-H) has 5107
 > > elements
 > > Group 3 ( C-alpha) has 623
 > > elements
 > > Group 4 ( Backbone) has 1869
 > > elements
 > > Group 5 ( MainChain) has 2488
 > > elements
 > > Group 6 (MainChain+Cb) has 3083
 > > elements
 > > Group 7 ( MainChain+H) has 3099
 > > elements
 > > Group 8 ( SideChain) has 7115
 > > elements
 > > Group 9 ( SideChain-H) has 2619 elements
 > > Group 10 ( Prot-Masses) has 10214 elements
 > > Group 11 ( Non-Protein) has 59842 elements
 > > Group 12 ( ATP) has 43 elements
 > > Group 13 ( SOL) has 59799 elements
 > > Group 14 ( Other) has 59842 elements
 > > Select a group: 13
 > > Selected 13: 'SOL'
 > > Number of (3-atomic) solvent molecules: 19933
 > >
 > > Processing topology
 > >
 > > Back Off! I just backed up temp.top to ./#temp.top.1#
 > >
 > > ---
 > > Program genion, VERSION 4.0.7
 > > Source code file: gmx_genion.c, line: 269
 > >
 > > Software inconsistency error:
 > > Not enough water
 > > ---
 > >
 > > Though my system has sufficient amount of water (19933) molecules.
 > > Can not understand the error. Any information would be useful.
 > >
 > >
 > > Chadan
 > > --
 > > Chandan kumar Choudhury
 > > NCL, Pune
 > > INDIA
 > >
 > > 


 > > Express yourself instantly with MSN Messenger! MSN Messenger
 > > 
 > >
 > > --
 > > gmx-users mailing list gmx-users@gromacs.org
 > > 
 > > http://lists.gromacs.org/mailman/listinfo/gm

RE: [gmx-users] Software inconsistency error: Not enough water

[Berk Hess]

Hi,

Yes, but genion is not smart enough (yet) to see the difference between crystal 
water and normal water.

Berk

> Date: Thu, 11 Feb 2010 13:07:41 +
> From: t.pig...@bristol.ac.uk
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> 
> Plus I suppose that if you have kept the crystal waters you would not 
> want them to be replaced by genion.
> 
> Tom
> 
> Berk Hess wrote:
> > Hi,
> > 
> > We are getting to much detail now.
> > In principle yes, but since you get a clear error message now, I 
> > wouldn't worry about this.
> > The chance that the last water block is willingly smaller than the 
> > number of ions is about zero.
> > 
> > Berk
> > 
> >  > Date: Thu, 11 Feb 2010 13:34:59 +0100
> >  > From: er...@xray.bmc.uu.se
> >  > To: gmx-users@gromacs.org
> >  > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> >  >
> >  > Hi,
> >  >
> >  > Is it desirable that genion only considers a single SOL block? Why not
> >  > use them all if there are many?
> >  >
> >  > Regards,
> >  >
> >  > Erik
> >  >
> >  > Berk Hess skrev:
> >  > > Hi,
> >  > >
> >  > > genion in future Gromacs versions will only use the last SOL block
> >  > > and give a proper error message when there is not enough water.
> >  > >
> >  > > Berk
> >  > >
> >  > > 
> > 
> >  > > From: iitd...@gmail.com
> >  > > Date: Thu, 11 Feb 2010 16:45:06 +0530
> >  > > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> >  > > To: gmx-users@gromacs.org
> >  > >
> >  > >
> >  > > Thanks berk.
> >  > > By the way, if I dont give -p topol.top as input to genion, then
> >  > > genion executes. In this case, I manually edit the topology file and
> >  > > add the ion information.
> >  > > [ molecules ]
> >  > > ; Compound #mols
> >  > > Protein_A 1
> >  > > Protein_B 1
> >  > > Protein_C 1
> >  > > Protein_D 1
> >  > > Protein_E 1
> >  > > SOL 32
> >  > > SOL 46
> >  > > SOL 3
> >  > > SOL 13
> >  > > SOL 19791
> >  > > Na 48
> >  > >
> >  > > This is my part of topology after adding ions (Na). In the previous
> >  > > case of genion was only considering first SOL information, which has
> >  > > only 32 molecules.
> >  > >
> >  > > Chandan
> >  > >
> >  > >
> >  > > --
> >  > > Chandan kumar Choudhury
> >  > > NCL, Pune
> >  > > INDIA
> >  > >
> >  > >
> >  > > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  >  > > > wrote:
> >  > >
> >  > > Hi,
> >  > >
> >  > > This error message in incorrect, it is probably not a software
> >  > > inconsistency.
> >  > > Looking at the code, it seems the problem is that the topology file
> >  > > you provided does not have enough SOL molecules in the [molecules
> >  > > ] section.
> >  > > I'll fix this error message for the next release.
> >  > >
> >  > > Berk
> >  > >
> >  > > 
> > 
> >  > > From: iitd...@gmail.com 
> >  > > Date: Thu, 11 Feb 2010 12:48:53 +0530
> >  > > To: gmx-users@gromacs.org 
> >  > > Subject: [gmx-users] Software inconsistency error: Not enough water
> >  > >
> >  > >
> >  > > Hello gmxusers !!
> >  > > I am simulating a protein and it is bound to ATP.
> >  > > Simulation of protein alone (without) works fine. Solely ATP
> >  > > simulation too works. But the problem arises on adding ions to the
> >  > > protein + ATP (1QHH.pdb) file.
> >  > > Error:
> >  > >
> >  > >
> >  > > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48
> >  > > WARNING: turning of free energy, will use lambda=0
> >  > > Reading file em.tpr, VERSION 4.0.7 (single precision)
> >  > > Using a coulomb cut-off of 0.9 nm
> >  > > Will try to add 48 Na ions and 0 Cl ions.
> >  > > Select a continuous group of solvent molecules
> >  > > Opening library file
> >  > > /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> >  > > Group 0 ( System) has 70056
> >  > > elements
> >  > > Group 1 ( Protein) has 10214
> >  > > elements
> >  > > Group 2 ( Protein-H) has 5107
> >  > > elements
> >  > > Group 3 ( C-alpha) has 623
> >  > > elements
> >  > > Group 4 ( Backbone) has 1869
> >  > > elements
> >  > > Group 5 ( MainChain) has 2488
> >  > > elements
> >  > > Group 6 (MainChain+Cb) has 3083
> >  > > elements
> >  > > Group 7 ( MainChain+H) has 3099
> >  > > elements
> >  > > Group 8 ( SideChain) has 7115
> >  > > elements
> >  > > Group 9 ( SideChain-H) has 2619 elements
> >  > > Group 10 ( Prot-Masses) has 10214 elements
> >  > > Group 11 ( Non-Protein) has 59842 elements
> >  > > Group 12 ( ATP) has 43 elements
> >  > > Group 13 ( SOL) has 59799 elements
> >  > > Group 14 ( Other) has 59842 elements
> >  > > Select a group: 13
> >  > > Selected 13: 'SOL'
> >  > > Number of (3-atomic) solvent molecules: 19933
> >  > >
> >  > > Processing topology
> >  > >
> >  > > Back Off! I just backed up temp.top to ./#temp.top.1#

Re: [gmx-users] Software inconsistency error: Not enough water

[Thomas Piggot]

Sure, that's why I think it is a good idea to do what you said and just 
have genion use the final SOL block (normally added through genbox, so 
not containing the crystal waters) rather than use all of the SOL blocks.


Tom

Berk Hess wrote:

Hi,

Yes, but genion is not smart enough (yet) to see the difference between 
crystal water and normal water.


Berk

 > Date: Thu, 11 Feb 2010 13:07:41 +
 > From: t.pig...@bristol.ac.uk
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
 >
 > Plus I suppose that if you have kept the crystal waters you would not
 > want them to be replaced by genion.
 >
 > Tom
 >
 > Berk Hess wrote:
 > > Hi,
 > >
 > > We are getting to much detail now.
 > > In principle yes, but since you get a clear error message now, I
 > > wouldn't worry about this.
 > > The chance that the last water block is willingly smaller than the
 > > number of ions is about zero.
 > >
 > > Berk
 > >
 > > > Date: Thu, 11 Feb 2010 13:34:59 +0100
 > > > From: er...@xray.bmc.uu.se
 > > > To: gmx-users@gromacs.org
 > > > Subject: Re: [gmx-users] Software inconsistency error: Not enough 
water

 > > >
 > > > Hi,
 > > >
 > > > Is it desirable that genion only considers a single SOL block? 
Why not

 > > > use them all if there are many?
 > > >
 > > > Regards,
 > > >
 > > > Erik
 > > >
 > > > Berk Hess skrev:
 > > > > Hi,
 > > > >
 > > > > genion in future Gromacs versions will only use the last SOL block
 > > > > and give a proper error message when there is not enough water.
 > > > >
 > > > > Berk
 > > > >
 > > > >
 > > 


 > > > > From: iitd...@gmail.com
 > > > > Date: Thu, 11 Feb 2010 16:45:06 +0530
 > > > > Subject: Re: [gmx-users] Software inconsistency error: Not 
enough water

 > > > > To: gmx-users@gromacs.org
 > > > >
 > > > >
 > > > > Thanks berk.
 > > > > By the way, if I dont give -p topol.top as input to genion, then
 > > > > genion executes. In this case, I manually edit the topology 
file and

 > > > > add the ion information.
 > > > > [ molecules ]
 > > > > ; Compound #mols
 > > > > Protein_A 1
 > > > > Protein_B 1
 > > > > Protein_C 1
 > > > > Protein_D 1
 > > > > Protein_E 1
 > > > > SOL 32
 > > > > SOL 46
 > > > > SOL 3
 > > > > SOL 13
 > > > > SOL 19791
 > > > > Na 48
 > > > >
 > > > > This is my part of topology after adding ions (Na). In the previous
 > > > > case of genion was only considering first SOL information, 
which has

 > > > > only 32 molecules.
 > > > >
 > > > > Chandan
 > > > >
 > > > >
 > > > > --
 > > > > Chandan kumar Choudhury
 > > > > NCL, Pune
 > > > > INDIA
 > > > >
 > > > >
 > > > > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  > > > > wrote:
 > > > >
 > > > > Hi,
 > > > >
 > > > > This error message in incorrect, it is probably not a software
 > > > > inconsistency.
 > > > > Looking at the code, it seems the problem is that the topology file
 > > > > you provided does not have enough SOL molecules in the [molecules
 > > > > ] section.
 > > > > I'll fix this error message for the next release.
 > > > >
 > > > > Berk
 > > > >
 > > > >
 > > 


 > > > > From: iitd...@gmail.com 
 > > > > Date: Thu, 11 Feb 2010 12:48:53 +0530
 > > > > To: gmx-users@gromacs.org 
 > > > > Subject: [gmx-users] Software inconsistency error: Not enough water
 > > > >
 > > > >
 > > > > Hello gmxusers !!
 > > > > I am simulating a protein and it is bound to ATP.
 > > > > Simulation of protein alone (without) works fine. Solely ATP
 > > > > simulation too works. But the problem arises on adding ions to the
 > > > > protein + ATP (1QHH.pdb) file.
 > > > > Error:
 > > > >
 > > > >
 > > > > $ genion -s em.tpr -o ion.pdb -p topol.top -np 48
 > > > > WARNING: turning of free energy, will use lambda=0
 > > > > Reading file em.tpr, VERSION 4.0.7 (single precision)
 > > > > Using a coulomb cut-off of 0.9 nm
 > > > > Will try to add 48 Na ions and 0 Cl ions.
 > > > > Select a continuous group of solvent molecules
 > > > > Opening library file
 > > > > /usr/local/gromacs/share/gromacs/top/aminoacids.dat
 > > > > Group 0 ( System) has 70056
 > > > > elements
 > > > > Group 1 ( Protein) has 10214
 > > > > elements
 > > > > Group 2 ( Protein-H) has 5107
 > > > > elements
 > > > > Group 3 ( C-alpha) has 623
 > > > > elements
 > > > > Group 4 ( Backbone) has 1869
 > > > > elements
 > > > > Group 5 ( MainChain) has 2488
 > > > > elements
 > > > > Group 6 (MainChain+Cb) has 3083
 > > > > elements
 > > > > Group 7 ( MainChain+H) has 3099
 > > > > elements
 > > > > Group 8 ( SideChain) has 7115
 > > > > elements
 > > > > Group 9 ( SideChain-H) has 2619 elements
 > > > > Group 10 ( Prot-Masses) has 10214 elements
 > > > > Group 11 ( Non-Protein) has 59842 elements
 > > > > Group 12 ( ATP) has 43 elements
 > > > > Group 13 ( SOL) has 59799 elemen

[gmx-users] Re: 1. Need small well known QM/MM example (Ake Sandgren)

[Gerrit Groenhof]

Hi Ake,
you can download two files at 

wwwuser.gwdg.de/~ggroenh/ffamber03.tar.gz and 
wwwuser.gwdg.de/~ggroenh/qmmm_input.tar.gz 

First is the forcefield files (GMXLIB shoul point there)
second is qmmm input files for a QM/MM simulation.

Hope it helps.

Gerrit

> 
> Message: 1
> Date: Thu, 11 Feb 2010 10:05:56 +0100
> From: Ake Sandgren 
> Subject: [gmx-users] Need small well known QM/MM example
> To: gmx-users@gromacs.org
> Message-ID: <1265879156.17090.242.ca...@skalman.hpc2n.umu.se>
> Content-Type: text/plain
> 
> Hi!
> 
> I need a small QM/MM gromacs input data with a well known result (and
> preferably the output too) to compare to the gromacs/gamess-uk setup i'm
> testing.
> 
> Does anyone have something i can use?
> 
> -- 
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> 
> 
> 

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RE: [gmx-users] Software inconsistency error: Not enough water

[Berk Hess]

Hi,

Yes, but there are (currently) two independent steps in genion.
First water is replaced using the index group that the users selected
and then the top file is edited. They two steps are independent.
There are no checks that the index group actually matches the topology
molecule sections (and strictly speaking they don't have to either).
But it would be better to link the two steps, although I don't think I want
to spend more time on this.

Berk

> Date: Thu, 11 Feb 2010 13:29:06 +
> From: t.pig...@bristol.ac.uk
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> 
> Sure, that's why I think it is a good idea to do what you said and just 
> have genion use the final SOL block (normally added through genbox, so 
> not containing the crystal waters) rather than use all of the SOL blocks.
> 
> Tom
> 
> Berk Hess wrote:
> > Hi,
> > 
> > Yes, but genion is not smart enough (yet) to see the difference between 
> > crystal water and normal water.
> > 
> > Berk
> > 
> >  > Date: Thu, 11 Feb 2010 13:07:41 +
> >  > From: t.pig...@bristol.ac.uk
> >  > To: gmx-users@gromacs.org
> >  > Subject: Re: [gmx-users] Software inconsistency error: Not enough water
> >  >
> >  > Plus I suppose that if you have kept the crystal waters you would not
> >  > want them to be replaced by genion.
> >  >
> >  > Tom
> >  >
> >  > Berk Hess wrote:
> >  > > Hi,
> >  > >
> >  > > We are getting to much detail now.
> >  > > In principle yes, but since you get a clear error message now, I
> >  > > wouldn't worry about this.
> >  > > The chance that the last water block is willingly smaller than the
> >  > > number of ions is about zero.
> >  > >
> >  > > Berk
> >  > >
> >  > > > Date: Thu, 11 Feb 2010 13:34:59 +0100
> >  > > > From: er...@xray.bmc.uu.se
> >  > > > To: gmx-users@gromacs.org
> >  > > > Subject: Re: [gmx-users] Software inconsistency error: Not enough 
> > water
> >  > > >
> >  > > > Hi,
> >  > > >
> >  > > > Is it desirable that genion only considers a single SOL block? 
> > Why not
> >  > > > use them all if there are many?
> >  > > >
> >  > > > Regards,
> >  > > >
> >  > > > Erik
> >  > > >
> >  > > > Berk Hess skrev:
> >  > > > > Hi,
> >  > > > >
> >  > > > > genion in future Gromacs versions will only use the last SOL block
> >  > > > > and give a proper error message when there is not enough water.
> >  > > > >
> >  > > > > Berk
> >  > > > >
> >  > > > >
> >  > > 
> > 
> >  > > > > From: iitd...@gmail.com
> >  > > > > Date: Thu, 11 Feb 2010 16:45:06 +0530
> >  > > > > Subject: Re: [gmx-users] Software inconsistency error: Not 
> > enough water
> >  > > > > To: gmx-users@gromacs.org
> >  > > > >
> >  > > > >
> >  > > > > Thanks berk.
> >  > > > > By the way, if I dont give -p topol.top as input to genion, then
> >  > > > > genion executes. In this case, I manually edit the topology 
> > file and
> >  > > > > add the ion information.
> >  > > > > [ molecules ]
> >  > > > > ; Compound #mols
> >  > > > > Protein_A 1
> >  > > > > Protein_B 1
> >  > > > > Protein_C 1
> >  > > > > Protein_D 1
> >  > > > > Protein_E 1
> >  > > > > SOL 32
> >  > > > > SOL 46
> >  > > > > SOL 3
> >  > > > > SOL 13
> >  > > > > SOL 19791
> >  > > > > Na 48
> >  > > > >
> >  > > > > This is my part of topology after adding ions (Na). In the previous
> >  > > > > case of genion was only considering first SOL information, 
> > which has
> >  > > > > only 32 molecules.
> >  > > > >
> >  > > > > Chandan
> >  > > > >
> >  > > > >
> >  > > > > --
> >  > > > > Chandan kumar Choudhury
> >  > > > > NCL, Pune
> >  > > > > INDIA
> >  > > > >
> >  > > > >
> >  > > > > On Thu, Feb 11, 2010 at 3:38 PM, Berk Hess  >  > > > > > wrote:
> >  > > > >
> >  > > > > Hi,
> >  > > > >
> >  > > > > This error message in incorrect, it is probably not a software
> >  > > > > inconsistency.
> >  > > > > Looking at the code, it seems the problem is that the topology file
> >  > > > > you provided does not have enough SOL molecules in the [molecules
> >  > > > > ] section.
> >  > > > > I'll fix this error message for the next release.
> >  > > > >
> >  > > > > Berk
> >  > > > >
> >  > > > >
> >  > > 
> > 
> >  > > > > From: iitd...@gmail.com 
> >  > > > > Date: Thu, 11 Feb 2010 12:48:53 +0530
> >  > > > > To: gmx-users@gromacs.org 
> >  > > > > Subject: [gmx-users] Software inconsistency error: Not enough water
> >  > > > >
> >  > > > >
> >  > > > > Hello gmxusers !!
> >  > > > > I am simulating a protein and it is bound to ATP.
> >  > > > > Simulation of protein alone (without) works fine. Solely ATP
> >  > > > > simulation too works. But the problem arises on adding ions to the
> >  > > > > protein + ATP (1QHH.pdb) file.
> >  > > > > Error:
> >  > > > >
> >  > > > >
> >  > > > > $ genion -s em.

Re: [gmx-users] Re: 1. Need small well known QM/MM example (Ake Sandgren)

[Ake Sandgren]

On Thu, 2010-02-11 at 14:41 +0100, Gerrit Groenhof wrote:
> Hi Ake,
> you can download two files at 
> 
> wwwuser.gwdg.de/~ggroenh/ffamber03.tar.gz and 
> wwwuser.gwdg.de/~ggroenh/qmmm_input.tar.gz 
> 
> First is the forcefield files (GMXLIB shoul point there)
> second is qmmm input files for a QM/MM simulation.

Ok.
Do you have the outputs from a known good run of them too to compare
with?

And I would also like a set of instructions on how run this since I'm
not a real Gromacs user and would easily make mistakes. (Just a sysadmin
trying to get things to work :-)

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

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[gmx-users] Problem with OPLS Benzene and Bond Constraints

[Mike Wykes]

Dear All

I would like to perform MD simulations with benzene as a solvent and
am observing some strange behaviour when I use Lincs to constrain all
the bonds. When I run a fully flexible NPT MD of a box of 320 benzene
molecules simulation at 298K and 1bar, the density comes out at  841
g/l, not too far away from the experimental value of 876 g/l. However
when I constrain all bonds using Lincs, the system expands rapidly,
stabilising at a density of  2.62 g/l ! Both simulations started from
NVT equilibrated simulations fixed to the experimental density. In the
papers describing OPLS parametrisation, the MC simulations were indeed
performed with fully flexible molecules, but it surprises me that the
bond constraints would affect the density so strongly. Does anyone
have any ideas why this is occurring? I am using a cutoff of 1.5 nm
for VDW and Coulomb interactions without EWALD/PME but this is
consistent with how OPLS was parametrised. There are no Lincs warnings
in the log file of the constrained simulation.

Please find my mdp and Benzene itp files below, the only difference
between the flexible and constrained runs being dt = 0.001/0.002 and
constraints = none/all-bonds respectively.

Many thanks for your ideas/explanations as to what could be going on,

Mike

;
;   File 'mdout.mdp' was generated
;   By user: mwykes (7017)
;   On host: node168
;   At date: Thu Feb  4 20:05:46 2010
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   = -DFLEX_SPC

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.002
nsteps   = 500
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm-mode= LINEAR
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 1.0
emstep   = 0.1
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 500
nstenergy= 500
; Output frequency and precision for xtc file
nstxtcout= 500
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = BNZ
; Selection of energy groups
energygrps   = BNZ

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
nstype   = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.5

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r= 1
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for cal

Re: [gmx-users] Problem with OPLS Benzene and Bond Constraints

[Ran Friedman]

Dear Mike,

It's hard to know what's going on from your input. Did you check the
thermodynamic components with g_energy (especially the pressure bond, LJ
and Coulomb energies)? This may give you a hint. Also, I would do a test
run with PME - you're anyway not following the parametrisation of
Jorgensen and co-workers exactly. As a final note - the correct phase is
something that's very difficult to reproduce exactly with classical MD,
and while a single molecule interacting with a protein may work just
fine, a bulk of such molecules does not always reproduce the correct
phase at a given temperature. This is one reason why lipid models are
still being developed.

Hope that helps a bit,
Ran

Mike Wykes wrote:
> Dear All
>
> I would like to perform MD simulations with benzene as a solvent and
> am observing some strange behaviour when I use Lincs to constrain all
> the bonds. When I run a fully flexible NPT MD of a box of 320 benzene
> molecules simulation at 298K and 1bar, the density comes out at  841
> g/l, not too far away from the experimental value of 876 g/l. However
> when I constrain all bonds using Lincs, the system expands rapidly,
> stabilising at a density of  2.62 g/l ! Both simulations started from
> NVT equilibrated simulations fixed to the experimental density. In the
> papers describing OPLS parametrisation, the MC simulations were indeed
> performed with fully flexible molecules, but it surprises me that the
> bond constraints would affect the density so strongly. Does anyone
> have any ideas why this is occurring? I am using a cutoff of 1.5 nm
> for VDW and Coulomb interactions without EWALD/PME but this is
> consistent with how OPLS was parametrised. There are no Lincs warnings
> in the log file of the constrained simulation.
>
> Please find my mdp and Benzene itp files below, the only difference
> between the flexible and constrained runs being dt = 0.001/0.002 and
> constraints = none/all-bonds respectively.
>
> Many thanks for your ideas/explanations as to what could be going on,
>
> Mike
>
> ;
> ;   File 'mdout.mdp' was generated
> ;   By user: mwykes (7017)
> ;   On host: node168
> ;   At date: Thu Feb  4 20:05:46 2010
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS
> ; Preprocessor information: use cpp syntax.
> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
> include  =
> ; e.g.: -DI_Want_Cookies -DMe_Too
> define   = -DFLEX_SPC
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.002
> nsteps   = 500
> ; For exact run continuation or redoing part of a run
> ; Part index is updated automatically on checkpointing (keeps files separate)
> simulation_part  = 1
> init_step= 0
> ; mode for center of mass motion removal
> comm-mode= LINEAR
> ; number of steps for center of mass motion removal
> nstcomm  = 1
> ; group(s) for center of mass motion removal
> comm-grps=
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric  = 0
> ld-seed  = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol= 1.0
> emstep   = 0.1
> ; Max number of iterations in relax_shells
> niter= 20
> ; Step size (ps^2) for minimization of flexible constraints
> fcstep   = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep   = 1000
> nbfgscorr= 10
>
> ; TEST PARTICLE INSERTION OPTIONS
> rtpi = 0.05
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> ; Output frequency for energies to log file and energy file
> nstlog   = 500
> nstenergy= 500
> ; Output frequency and precision for xtc file
> nstxtcout= 500
> xtc-precision= 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps = BNZ
> ; Selection of energy groups
> energygrps   = BNZ
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 10
> ; ns algorithm (simple or grid)
> nstype   = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc  = xyz
> periodic_molecules   = no
> ; nblist cut-off
> rlist= 1.5
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = Cut-off
> rcoulomb-switch  = 0
> rcoulomb = 1.5
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r= 1
> epsilon_rf  

[gmx-users] intrapeptide hbond existence map

[ABEL Stephane 175950]

Hi everybody, 

I am doing some analysis of the interpeptidique hbonds (INTRHB) during the 
aggregation in beta fuof 4 heptapeptides in water 

I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 
28 INTRHB like this 

NH--CO


[intra_hbds]
4 17 5
18 26 19
27 43 28
44 52 45
53 60 54


to obtain the INTRHB existence map i used the command with gmx4.05

g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f 
./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 
4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map

The map show in the x and y axis the time and residue (up to 84). I have no 
idea what the figure means. The olot is stored here 
http://www.st-abel.com/Hbond_occupency.jpg

I want only to know if, for example, the Hbond_occupency for the group NH or CO 
of the residu 1 

Thank you in advance for your help

Stephane






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Re: [gmx-users] intrapeptide hbond existence map

[Justin A. Lemkul]

ABEL Stephane 175950 wrote:
Hi everybody, 

I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water 

I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this 


NH--CO


[intra_hbds]
4 17 5
18 26 19
27 43 28
44 52 45
53 60 54


to obtain the INTRHB existence map i used the command with gmx4.05

g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f 
./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 
4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map

The map show in the x and y axis the time and residue (up to 84). I have no 
idea what the figure means. The olot is stored here 
http://www.st-abel.com/Hbond_occupency.jpg

I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 



The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the 
donor-acceptor pairs to the plot.  Find within that index file a directive that 
starts with "hbonds" that corresponds to all of the H-bonds that were found, and 
thus plotted.  Red indicates the H-bond exists, white means it doesn't.  As for 
occupancy, you'd probably have to script that to parse the .xpm file and 
calculate a percentage of frames for when the particular H-bond exists, or get 
lifetimes from g_hbond.


-Justin


Thank you in advance for your help

Stephane









--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] intrapeptide hbond existence map

[Ran Friedman]

Hi Stephane,

The map shows weather a certain hydrogen bond exists at a certain time.
In principle you can get the information by integrating this data, but
I'm not sure it can be done without changing the code. A possible
solution is to use a script and run g_hbond -num 28 times with two
relevant groups (N-H  donor and oxygen acceptor), and calculate the
occupancy based on this (I guess you mean the fraction of time that this
h_bond existed.

Ran.

ABEL Stephane 175950 wrote:
> Hi everybody, 
>
> I am doing some analysis of the interpeptidique hbonds (INTRHB) during the 
> aggregation in beta fuof 4 heptapeptides in water 
>
> I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 
> 28 INTRHB like this 
>
> NH--CO
>
>
> [intra_hbds]
> 4 17 5
> 18 26 19
> 27 43 28
> 44 52 45
> 53 60 54
> 
>
> to obtain the INTRHB existence map i used the command with gmx4.05
>
> g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f 
> ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 
> 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map
>
> The map show in the x and y axis the time and residue (up to 84). I have no 
> idea what the figure means. The olot is stored here 
> http://www.st-abel.com/Hbond_occupency.jpg
>
> I want only to know if, for example, the Hbond_occupency for the group NH or 
> CO of the residu 1 
>
> Thank you in advance for your help
>
> Stephane
>   

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Re: [gmx-users] intrapeptide hbond existence map

[Erik Marklund]

Justin A. Lemkul skrev:



ABEL Stephane 175950 wrote:

Hi everybody,
I am doing some analysis of the interpeptidique hbonds (INTRHB) 
during the aggregation in beta fuof 4 heptapeptides in water
I have defined in a index file the Acceptor-Donor-Hydrogen atoms list 
for the 28 INTRHB like this

NH--CO


[intra_hbds]
4 17 5
18 26 19
27 43 28
44 52 45
53 60 54


to obtain the INTRHB existence map i used the command with gmx4.05

g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f 
./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 
4_Peptide_53A6_hbonds_400_500ns_index -hbm 
4_Peptide_53A6_hbonds_400_500ns_Map


The map show in the x and y axis the time and residue (up to 84). I 
have no idea what the figure means. The olot is stored here 
http://www.st-abel.com/Hbond_occupency.jpg


I want only to know if, for example, the Hbond_occupency for the 
group NH or CO of the residu 1


The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the 
donor-acceptor pairs to the plot. Find within that index file a 
directive that starts with "hbonds" that corresponds to all of the 
H-bonds that were found, and thus plotted. Red indicates the H-bond 
exists, white means it doesn't. As for occupancy, you'd probably have 
to script that to parse the .xpm file and calculate a percentage of 
frames for when the particular H-bond exists, or get lifetimes from 
g_hbond.


-Justin
…or to define smaller index groups, e.g. the NH- or CO-group of res 1, 
and get the number of hydrogen bonds as function of time from the -num 
output (default is hbnum.xvg). You would have to repeat this for all 
(reasonable combinations of) hbonding groups that you're interested in, 
which can result in maaany g_hbond executions. But if the number of 
groups are small, then it's certainly doable. It seems from your plot 
though, that scripted processing of the -hbm and -hbn output, as Justin 
suggests, is the way to go here. Make sure you're matching the index 
file to the xpm file in the right way! I've made mistakes in that area 
myself.


Erik




Thank you in advance for your help

Stephane












--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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[gmx-users] Working with Reduced Units

[Lum Nforbi]

Hi all,

   Please, can someone shed more light on how to set up reduced units in
an .mdp file? I have tried to this but it does not work. I set epsilon,
sigma and mass to 1 in my force field file as stated in section 2.3 of the
manual. I multiplied 300K temperature by 0.00831451 and divided by epsilon
to get a temperature in reduced units with value 2.5. I also calculated the
pressure of 1bar in reduced units as shown on Table 2.4 of the manual to get
a value of 0.0431 and included all of these in the .mdp file but this did
not work for me in the mdrun.
  Is this the right way to set up reduced units in gromacs? Please, help
me out.

Thanks,
Lum
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[gmx-users] different results in different machines

[Rebeca García Fandiño]

Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very 
different results using 2 different machines.  Attached you can see that the
graphics are really different for both cases (about 10 KJ/mol!!). The version
of Gromacs (3.3.3) and number of processors used (2) is the same for
both calculations. The .tpr files and all the starting files are
identical for both calculations. The only thing that changes is the
machine where they were carried out. 

I have checked the energy files for both cases, and they are different,
but taking into account the stochastic effect, I suppose it is normal.
There are slight differences in the energies in the step 0 for some of
the windows (but in the 5th decimal number, so they should not be
important, I suppose). Any idea of the cause of the problem? Has
anyone experienced similar problems? Any suggestion will be much appreciated.

Thanks a lot for your help, in advance.

Cheers,


Rebeca Garcia 

  
_
¿Aún no sabes qué móvil eres? ¡Descúbrelo aquí!
http://www.quemovileres.com/

comparation_neuron_ngs.pdf
Description: Adobe PDF document
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Re: [gmx-users] different results in different machines

[David van der Spoel]

On 2/11/10 7:40 PM, Rebeca García Fandiño wrote:

Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very 
different results using 2 different machines.  Attached you can see 
that the graphics are really different for both cases (about 10 
KJ/mol!!). The version of Gromacs (3.3.3) and number of processors 
used (2) is the same for both calculations. The .tpr files and all the 
starting files are identical for both calculations. The only thing 
that changes is the machine where they were carried out.
I have checked the energy files for both cases, and they are 
different, but taking into account the stochastic effect, I suppose it 
is normal. There are slight differences in the energies in the step 0 
for some of the windows (but in the 5th decimal number, so they should 
not be important, I suppose). Any idea of the cause of the problem? 
Has anyone experienced similar problems? Any suggestion will be much 
appreciated.

Thanks a lot for your help, in advance.
Cheers,
Without error bars it is very hard to judge how different these are. Can 
you add errorbars?

How long are the simulations at the individual data points?


Rebeca Garcia



Elige un juego de Messenger. Reta a un amigo. ¡Pruébalo ya! 




--
David.

David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://xray.bmc.uu.se/~spoel


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[gmx-users] intrapeptide hbond existence map

[ABEL Stephane 175950]

Ok thank you all for your suggestions

A bientot


>
> ABEL Stephane 175950 wrote:
>> Hi everybody,
>> I am doing some analysis of the interpeptidique hbonds (INTRHB) 
>> during the aggregation in beta fuof 4 heptapeptides in water
>> I have defined in a index file the Acceptor-Donor-Hydrogen atoms list 
>> for the 28 INTRHB like this
>> NH--CO
>>
>>
>> [intra_hbds]
>> 4 17 5
>> 18 26 19
>> 27 43 28
>> 44 52 45
>> 53 60 54
>> 
>>
>> to obtain the INTRHB existence map i used the command with gmx4.05
>>
>> g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f 
>> ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 
>> 4_Peptide_53A6_hbonds_400_500ns_index -hbm 
>> 4_Peptide_53A6_hbonds_400_500ns_Map
>>
>> The map show in the x and y axis the time and residue (up to 84). I 
>> have no idea what the figure means. The olot is stored here 
>> http://www.st-abel.com/Hbond_occupency.jpg
>>
>> I want only to know if, for example, the Hbond_occupency for the 
>> group NH or CO of the residu 1
>
> The output file "-hbn 4_Peptide_53A6_hbonds_400_500ns_index" maps the 
> donor-acceptor pairs to the plot. Find within that index file a 
> directive that starts with "hbonds" that corresponds to all of the 
> H-bonds that were found, and thus plotted. Red indicates the H-bond 
> exists, white means it doesn't. As for occupancy, you'd probably have 
> to script that to parse the .xpm file and calculate a percentage of 
> frames for when the particular H-bond exists, or get lifetimes from 
> g_hbond.
>
> -Justin
.or to define smaller index groups, e.g. the NH- or CO-group of res 1, 
and get the number of hydrogen bonds as function of time from the -num 
output (default is hbnum.xvg). You would have to repeat this for all 
(reasonable combinations of) hbonding groups that you're interested in, 
which can result in maaany g_hbond executions. But if the number of 
groups are small, then it's certainly doable. It seems from your plot 
though, that scripted processing of the -hbm and -hbn output, as Justin 
suggests, is the way to go here. Make sure you're matching the index 
file to the xpm file in the right way! I've made mistakes in that area 
myself.

Erik

>
>> Thank you in advance for your help
>>
>> Stephane
>>
>>
>>
>>
>>
>>
>>
>


-- 
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys



--

Message: 5
Date: Thu, 11 Feb 2010 09:49:42 -0800
From: Lum Nforbi 
Subject: [gmx-users] Working with Reduced Units
To: gmx-users@gromacs.org
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi all,

   Please, can someone shed more light on how to set up reduced units in
an .mdp file? I have tried to this but it does not work. I set epsilon,
sigma and mass to 1 in my force field file as stated in section 2.3 of the
manual. I multiplied 300K temperature by 0.00831451 and divided by epsilon
to get a temperature in reduced units with value 2.5. I also calculated the
pressure of 1bar in reduced units as shown on Table 2.4 of the manual to get
a value of 0.0431 and included all of these in the .mdp file but this did
not work for me in the mdrun.
  Is this the right way to set up reduced units in gromacs? Please, help
me out.

Thanks,
Lum
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Message: 6
Date: Thu, 11 Feb 2010 18:40:10 +
From: Rebeca Garc?a Fandi?o 
Subject: [gmx-users] different results in different machines
To: 
Message-ID: 
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Re: [gmx-users] different results in different machines

[XAvier Periole]

On Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño wrote:


Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found  
very different results using 2 different machines.  Attached you can  
see that the graphics are really different for both cases (about 10  
KJ/mol!!). The version of Gromacs (3.3.3) and number of processors  
used (2) is the same for both calculations. The .tpr files and all  
the starting files are identical for both calculations. The only  
thing that changes is the machine where they were carried out.
I have checked the energy files for both cases, and they are  
different, but taking into account the stochastic effect, I suppose  
it is normal. There are slight differences in the energies in the  
step 0 for some of the windows (but in the 5th decimal number, so  
they should not be important, I suppose).

Well this might be a problem but the 5th decimal is pretty far.
Any idea of the cause of the problem? Has anyone experienced similar  
problems? Any suggestion will be much appreciated.

Thanks a lot for your help, in advance.

the only thing you have left is that you have not sampled enought ... so
you have not reached convergence.
Did you try to repeat the calculation on the ame machine changing the
initial velocities ?


Cheers,

Rebeca Garcia


Elige un juego de Messenger. Reta a un amigo. ¡Pruébalo ya!  
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RE: [gmx-users] different results in different machines

[Rebeca García Fandiño]

Thank you very much for the suggestions. I will look carefully for the 
convergence of my PMF to see if it is the problem.
Cheers,
Rebeca.

From: x.peri...@rug.nl
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] different results in different machines
Date: Thu, 11 Feb 2010 20:00:32 +0100


On Feb 11, 2010, at 7:40 PM, Rebeca García Fandiño wrote:Hi,
I am doing PMF calculations using Gromacs 3.3.3, and I have found very 
different results using 2 different machines.  Attached you can see that the 
graphics are really different for both cases (about 10 KJ/mol!!). The version 
of Gromacs (3.3.3) and number of processors used (2) is the same for both 
calculations. The .tpr files and all the starting files are identical for both 
calculations. The only thing that changes is the machine where they were 
carried out. 
I have checked the energy files for both cases, and they are different, but 
taking into account the stochastic effect, I suppose it is normal. There are 
slight differences in the energies in the step 0 for some of the windows (but 
in the 5th decimal number, so they should not be important, I suppose). Well 
this might be a problem but the 5th decimal is pretty far.
Any idea of the cause of the problem? Has anyone experienced similar problems? 
Any suggestion will be much appreciated.
Thanks a lot for your help, in advance.
the only thing you have left is that you have not sampled enought ... soyou 
have not reached convergence.Did you try to repeat the calculation on the ame 
machine changing the initial velocities ?
Cheers,

Rebeca Garcia 


Elige un juego de Messenger. Reta a un amigo. ¡Pruébalo ya! 
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[gmx-users] Latest gmxtest in git

[Jess Bromley]

Dear All,

I have retrieved the latest version of the gmxtest regression tests
from git and run them against a newly installed GROMACS 4.0.7
installation.  Most of the tests pass, but there are a few problems
--- I know from the wiki that some problems are expected, but as a
sysadmin rather than a user am not competent to determine for myself
which are "safe fails".  Can anybody tell me if any of the following
fails from the git version of gmxtest indicate an incorrectly
functioning gromacs-4.0.7 installation?

Many Thanks!

Test failures:

Simple: all passed

Complex: following failures... (all others passed)

Testing field . . . FAILED. Check checkvir.out (264 errors) files in field
Testing tip4p . . . FAILED. Check checkvir.out (95 errors) files in tip4p
Testing water . . . FAILED. Check checkvir.out (145 errors),
checkforce.out (1939 errors) files in water

Kernel: all passed

pdb2gmx: following failures... (all others passed)

Index  Reference   This test   Error  Description
  11-34.5967-42.0952   0.0977748  1aml.pdb with G53a6 using
vsite=none and water=spc
  12-34.5967-42.0952   0.0977748  1aml.pdb with G53a6 using
vsite=none and water=spce


Further information:
Run on a 64-bit x86 linux installation (Ubuntu kernel
2.6.31-19-generic) with glibc-2.10.1.
A self-compiled vanilla gcc-3.4.6 was first installed and then used to
compile (statically) both gromacs and the following dependencies:
openmpi-1.4.1
fftw-3.2.2
gsl-1.13
libxml2-2.6.30
gromacs was built with single precision, mpi support and not linked to
X libraries

Log files can be supplied on request...
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Re: [gmx-users] concaternating remd trajectories using trjcat & demux

[Segun Jung]

Thanks Justin,


On Wed, Feb 10, 2010 at 8:49 PM, Justin A. Lemkul  wrote:

>
>
> Segun Jung wrote:
>
>> Dear gromacs users,
>>
>> I am trying to collect trajectories corresponding to each temperature by
>> using trjcat with demux.
>>
>> There were similar issues posted earlier, but I do not see the solution on
>> the problem I am facing following:
>>
>>
> Like what?  It will save time if you can post links to these "similar
> issues" to avoid posting non-solutions that have already been ruled out.
>
>
>  I have 64 replicas simulated using namd  in dcd trajectory format and
>> saved them in gromacs format (.trr) using vmd.
>>
>> I inspected the gromacs format trajectories by eyes in vmd and looked
>> fine. However, when I tried trjcat -f g*.trr -demux replica_index.xvg,
>>
>> the output looked weird. So I tested a small set of the trajectories
>> (using only replicas 0 to 8 and first two frames) and
>>
>> noticed that the output does not match to the replica_index.xvg file.
>>
>>
> If you ran your simulations with NAMD, how did you generate this file?  In
> Gromacs, one would run demux.pl on the md.log file.  I presume NAMD prints
> different output.
>
> I wrote a perl script which does the same job as demux.pl generating the
replica_index.xvg.

>
>
>> trjcat -f *g*.trr -demux replica_index.xvg
>>
>> replica_index.xvg
>>
>> 0 0 1 2 3 4 5 7 6
>>
>> 2 1 0 2 3 5 4 6 7
>>
>>
> If you analyzed replicas 0 to 8 (inclusive) then you should have an 8
> somewhere, right?


And I was testing 8 replicas (from 0 to 7).  Sorry about the confusion.

>
>
>
>> I am using Ubuntu (32bit) and the gromas version is 4.0.5.
>>
>> 0_trajout.xtc should have the 1st frame from replica 0 and 2nd frame from
>> replica 1, but both frames for 0_trajout.xtc are from the replica 0.
>>
>>
> This might go along with my comment above.  If there are nine replicas (0
> to 8), then there may be some mis-translation of the .xvg file.
>
>
>  It seems the index file does not cooperate properly with the trjcat and
>> -demux. Does anyone have clue about this?
>>
>>
> I know I can attest to demultiplexing working as advertised, so I assume
> intact trajectories with a correct index file should work properly.  You
> have a few variables to deal with: .dcd->.trr translation, however you
> generated the .xvg file, and if you've even told us the right number of
> replicas, among perhaps others.
>

I fixed a minor mistake in my perl script which generates replica_index.xvg
and it works fine except the time step 0 of input file (*.trr) is saved two
times in the output file (*.xtc) although rest of the trajectories are okay.


-Segun

>
> Also, what does gmxcheck tell you about each of the .trr files?  Do they
> contain what you would expect them to?
>
> -Justin
>
>
>> Many thanks,
>>
>> Segun
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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-- 
---
Segun Jung, Ph.D. Candidate
Computational Biology
Schlick Lab, Department of Chemistry
New York University
http://homepages.nyu.edu/~sj801

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[gmx-users] problems in setup the protein+ membrane

[chiloo777 777]

Dear all,

I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"

-Before this process, i've changed the ffG53a6nb.itp & ff53Ga6bon.itp
according to the tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)

my topology, you can see the attached files.
Thanks in advance
Jit




Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations

ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
  No default Proper Dih. types


---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)


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Re: [gmx-users] problems in setup the protein+ membrane

[Mark Abraham]

On 12/02/10 12:16, chiloo777 777 wrote:

Dear all,

I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"

-Before this process, i've changed the ffG53a6nb.itp&  ff53Ga6bon.itp
according to the tutorial
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)

my topology, you can see the attached files.
Thanks in advance
Jit




Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations

ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
   No default Proper Dih. types


If there's no default proper dihedral types defined, then you've 
#included things in a wrong order.


Mark



---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)



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Re: [gmx-users] problems in setup the protein+ membrane

[chiloo777 777]

Do you mean i should change the order of #include thing in file.top or
 something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?

Thanks
Jit

On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham  wrote:
> On 12/02/10 12:16, chiloo777 777 wrote:
>>
>> Dear all,
>>
>> I face some problem during run grompp (see below), the command is
>> "grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"
>>
>> -Before this process, i've changed the ffG53a6nb.itp&  ff53Ga6bon.itp
>> according to the tutorial
>>
>> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)
>>
>> my topology, you can see the attached files.
>> Thanks in advance
>> Jit
>>
>>
>>
>>
>> 
>> Ignoring obsolete mdp entry 'cpp'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
>> checking input for internal consistency...
>> processing topology...
>> Opening library file /usr/local/gromacs/share/top/ff_dum.itp
>> Generated 825 of the 2346 non-bonded parameter combinations
>>
>> ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
>>   No default Proper Dih. types
>
> If there's no default proper dihedral types defined, then you've #included
> things in a wrong order.
>
> Mark
>
>>
>> ---
>> Program grompp, VERSION 4.0.7
>> Source code file: toppush.c, line: 947
>>
>> Fatal error:
>> Atomtype HO not found
>> ---
>>
>> "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
>>
>>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] problems in setup the protein+ membrane

[Justin A. Lemkul]

chiloo777 777 wrote:

Do you mean i should change the order of #include thing in file.top or
 something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?



Without seeing your .top it's hard to give any really useful information.  All 
the bonded parameters for a given lipid should be included within the relevant 
.itp file.  If it's coming up as "not found" you're either using the wrong force 
field, not #including something at all, or your topology is otherwise 
incorrectly constructed.


-Justin


Thanks
Jit

On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham  wrote:

On 12/02/10 12:16, chiloo777 777 wrote:

Dear all,

I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"

-Before this process, i've changed the ffG53a6nb.itp&  ff53Ga6bon.itp
according to the tutorial

(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)

my topology, you can see the attached files.
Thanks in advance
Jit





Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations

ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
  No default Proper Dih. types

If there's no default proper dihedral types defined, then you've #included
things in a wrong order.

Mark


---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)



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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] problems in setup the protein+ membrane

[Justin A. Lemkul]

chiloo777 777 wrote:

To see topology, please see the attached files



You're using ffG53a6, per my tutorial, but then if you look within popg.itp, 
you'll find atom type HO, which is not a recognized type within 53a6 (it is for 
ffgmx).  The proper type is H.  The other warnings are probably due to some 
other similar force field type mismatch.  Identify which of these is problematic 
(grompp should print the line number in the topology), and assign suitable 
parameters.


As for this:

; Include water topology
#include "#include "/usr/local/gromacs/share/top/flexspc.itp"

I have no idea how that would even work, you don't even have proper closed 
quotes, but in any case you would only ever need:


#include "flexspc.itp"

...although you shouldn't be using a flexible water model for dynamics, anyway.

-Justin


Jit

On Fri, Feb 12, 2010 at 8:45 AM, Justin A. Lemkul  wrote:


chiloo777 777 wrote:

Do you mean i should change the order of #include thing in file.top or
 something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
& popg.itp?


Without seeing your .top it's hard to give any really useful information.
 All the bonded parameters for a given lipid should be included within the
relevant .itp file.  If it's coming up as "not found" you're either using
the wrong force field, not #including something at all, or your topology is
otherwise incorrectly constructed.

-Justin


Thanks
Jit

On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham 
wrote:

On 12/02/10 12:16, chiloo777 777 wrote:

Dear all,

I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o
b4ion.tpr"

-Before this process, i've changed the ffG53a6nb.itp&  ff53Ga6bon.itp
according to the tutorial


(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)

my topology, you can see the attached files.
Thanks in advance
Jit






Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations

ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
 No default Proper Dih. types

If there's no default proper dihedral types defined, then you've
#included
things in a wrong order.

Mark


---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Latest gmxtest in git

[Mark Abraham]

On 12/02/10 09:45, Jess Bromley wrote:

Dear All,

I have retrieved the latest version of the gmxtest regression tests
from git and run them against a newly installed GROMACS 4.0.7
installation.  Most of the tests pass, but there are a few problems
--- I know from the wiki that some problems are expected, but as a
sysadmin rather than a user am not competent to determine for myself
which are "safe fails".  Can anybody tell me if any of the following
fails from the git version of gmxtest indicate an incorrectly
functioning gromacs-4.0.7 installation?

Many Thanks!

Test failures:

Simple: all passed

Complex: following failures... (all others passed)

Testing field . . . FAILED. Check checkvir.out (264 errors) files in field
Testing tip4p . . . FAILED. Check checkvir.out (95 errors) files in tip4p
Testing water . . . FAILED. Check checkvir.out (145 errors),
checkforce.out (1939 errors) files in water

Kernel: all passed

pdb2gmx: following failures... (all others passed)

Index  Reference   This test   Error  Description
   11-34.5967-42.0952   0.0977748  1aml.pdb with G53a6 using
vsite=none and water=spc
   12-34.5967-42.0952   0.0977748  1aml.pdb with G53a6 using
vsite=none and water=spce


I haven't actually run 4.0.7 against git gmxtest, but I made the last 
commit to the latter, and it was routine for correctly-functioning 4.0.x 
versions to fail the tests you mention. I think your installation is fine.


Mark


Further information:
Run on a 64-bit x86 linux installation (Ubuntu kernel
2.6.31-19-generic) with glibc-2.10.1.
A self-compiled vanilla gcc-3.4.6 was first installed and then used to
compile (statically) both gromacs and the following dependencies:
openmpi-1.4.1
fftw-3.2.2
gsl-1.13
libxml2-2.6.30
gromacs was built with single precision, mpi support and not linked to
X libraries

Log files can be supplied on request...

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Re: [gmx-users] problems in setup the protein+ membrane

[chiloo777 777]

If this problem comes from the mismatch forcefield, That mean i should
change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is
matched with ffG53a6), right?

Thanks
Jit

On Fri, Feb 12, 2010 at 9:06 AM, Justin A. Lemkul  wrote:
>
>
> chiloo777 777 wrote:
>>
>> To see topology, please see the attached files
>>
>
> You're using ffG53a6, per my tutorial, but then if you look within popg.itp,
> you'll find atom type HO, which is not a recognized type within 53a6 (it is
> for ffgmx).  The proper type is H.  The other warnings are probably due to
> some other similar force field type mismatch.  Identify which of these is
> problematic (grompp should print the line number in the topology), and
> assign suitable parameters.
>
> As for this:
>
> ; Include water topology
> #include "#include "/usr/local/gromacs/share/top/flexspc.itp"
>
> I have no idea how that would even work, you don't even have proper closed
> quotes, but in any case you would only ever need:
>
> #include "flexspc.itp"
>
> ...although you shouldn't be using a flexible water model for dynamics,
> anyway.
>
> -Justin
>
>> Jit
>>
>> On Fri, Feb 12, 2010 at 8:45 AM, Justin A. Lemkul  wrote:
>>>
>>> chiloo777 777 wrote:

 Do you mean i should change the order of #include thing in file.top or
  something involving pope.itp?
 I try to change order of #include thing, there is the same error.
 Do i need to define something like "proper dihedral types" in pope.itp
 & popg.itp?

>>> Without seeing your .top it's hard to give any really useful information.
>>>  All the bonded parameters for a given lipid should be included within
>>> the
>>> relevant .itp file.  If it's coming up as "not found" you're either using
>>> the wrong force field, not #including something at all, or your topology
>>> is
>>> otherwise incorrectly constructed.
>>>
>>> -Justin
>>>
 Thanks
 Jit

 On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham 
 wrote:
>
> On 12/02/10 12:16, chiloo777 777 wrote:
>>
>> Dear all,
>>
>> I face some problem during run grompp (see below), the command is
>> "grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o
>> b4ion.tpr"
>>
>> -Before this process, i've changed the ffG53a6nb.itp&  ff53Ga6bon.itp
>> according to the tutorial
>>
>>
>>
>> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)
>>
>> my topology, you can see the attached files.
>> Thanks in advance
>> Jit
>>
>>
>>
>>
>>
>>
>> 
>> Ignoring obsolete mdp entry 'cpp'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
>> checking input for internal consistency...
>> processing topology...
>> Opening library file /usr/local/gromacs/share/top/ff_dum.itp
>> Generated 825 of the 2346 non-bonded parameter combinations
>>
>> ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
>>  No default Proper Dih. types
>
> If there's no default proper dihedral types defined, then you've
> #included
> things in a wrong order.
>
> Mark
>
>> ---
>> Program grompp, VERSION 4.0.7
>> Source code file: toppush.c, line: 947
>>
>> Fatal error:
>> Atomtype HO not found
>> ---
>>
>> "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
>>
>>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>


>>> --
>>> 
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> 
>>> --
>>> gmx-users mailing list    gmx-us...@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Depart

Re: [gmx-users] problems in setup the protein+ membrane

[Mark Abraham]

On 12/02/10 18:17, chiloo777 777 wrote:

If this problem comes from the mismatch forcefield, That mean i should
change forcefield from ffG53a6 to ffgmx, or find popg.itp (which is
matched with ffG53a6), right?


Standard procedure is to choose a forcefield that is known to be able to 
model the kind of system you're working on before you do anything else :-)


Mark


On Fri, Feb 12, 2010 at 9:06 AM, Justin A. Lemkul  wrote:



chiloo777 777 wrote:


To see topology, please see the attached files



You're using ffG53a6, per my tutorial, but then if you look within popg.itp,
you'll find atom type HO, which is not a recognized type within 53a6 (it is
for ffgmx).  The proper type is H.  The other warnings are probably due to
some other similar force field type mismatch.  Identify which of these is
problematic (grompp should print the line number in the topology), and
assign suitable parameters.

As for this:

; Include water topology
#include "#include "/usr/local/gromacs/share/top/flexspc.itp"

I have no idea how that would even work, you don't even have proper closed
quotes, but in any case you would only ever need:

#include "flexspc.itp"

...although you shouldn't be using a flexible water model for dynamics,
anyway.

-Justin


Jit

On Fri, Feb 12, 2010 at 8:45 AM, Justin A. Lemkul  wrote:


chiloo777 777 wrote:


Do you mean i should change the order of #include thing in file.top or
  something involving pope.itp?
I try to change order of #include thing, there is the same error.
Do i need to define something like "proper dihedral types" in pope.itp
&  popg.itp?


Without seeing your .top it's hard to give any really useful information.
  All the bonded parameters for a given lipid should be included within
the
relevant .itp file.  If it's coming up as "not found" you're either using
the wrong force field, not #including something at all, or your topology
is
otherwise incorrectly constructed.

-Justin


Thanks
Jit

On Fri, Feb 12, 2010 at 8:24 AM, Mark Abraham
wrote:


On 12/02/10 12:16, chiloo777 777 wrote:


Dear all,

I face some problem during run grompp (see below), the command is
"grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o
b4ion.tpr"

-Before this process, i've changed the ffG53a6nb.itp&ff53Ga6bon.itp
according to the tutorial



(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)

my topology, you can see the attached files.
Thanks in advance
Jit







Ignoring obsolete mdp entry 'cpp'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/top/ff_dum.itp
Generated 825 of the 2346 non-bonded parameter combinations

ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
  No default Proper Dih. types


If there's no default proper dihedral types defined, then you've
#included
things in a wrong order.

Mark


---
Program grompp, VERSION 4.0.7
Source code file: toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

"There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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