Re: [gmx-users] Error in pdb2gmx

[David van der Spoel]

vivek sharma wrote:

Hello there,
I am trying to run pdb2gmx on 3bzu.pdb file and got the following error

Opening library file /usr/share/gromacs/top/
ffG43b1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Reading 3bzu.pdb...
WARNING: all CONECT records are ignored
Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 
8581 atoms

Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file

---
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 878

Fatal error:
Chain identifier 'A' was used in two non-sequential blocks (residue 
1034, atom 7961)

---
 as I am new to this field. I'm finding it very difficult to find the 
reason and rectify it.

Any suggestion would be of great help..
This is a limitation in pdb2gmx. It expects the atoms in the chain A to 
be in sequence in the pdb file. You can manually sort the pdb file on 
the chain identifier.




With Thanx,
Vivek


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[gmx-users] requested for GROMACS package

[shiny chandy]

hello
I am working with protien 1PGB having 56 amino acids (practical tutorial
from GROMACS web site) for its simulation using the flexilbe water.
the commands that i have run are :

At later stsges of MD simulations ( i.e after position restrained MD), I
have been getting few errors which are as follow:
---
*./grompp –f run.mdp –p topol.top –c pr.gro –o run.tpr*
 followed by
*./mdrun –v –deffnm run*
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 .. 486 ]

---
this is my *run.mdp* file
integrator  = md
nsteps  = 5000
dt  = 0.002
nstlist = 10
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = Berendsen
tc-grps = protein non-protein
tau-t   = 0.1 0.1
ref-t   = 298 298
nstxout = 1000
nstvout = 1000
nstxtcout   = 100
nstenergy   = 100

what can i do in order to get rid of this error.
your help is kindly needed. In case if i need to give more  information,
please write back

shiny chandy
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Re: [gmx-users] requested for GROMACS package

[Justin A. Lemkul]

shiny chandy wrote:

hello
I am working with protien 1PGB having 56 amino acids (practical tutorial 
from GROMACS web site) for its simulation using the flexilbe water.

the commands that i have run are :

At later stsges of MD simulations ( i.e after position restrained MD), I 
have been getting few errors which are as follow:

---
*./grompp –f run.mdp –p topol.top –c pr.gro –o run.tpr*
 followed by
*./mdrun –v –deffnm run*
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 .. 486 ]

---
this is my _/*run.mdp*/_ file
integrator  = md
nsteps  = 5000
dt  = 0.002
nstlist = 10
rlist   = 1.0
coulombtype = pme
rcoulomb= 1.0
vdw-type= cut-off
rvdw= 1.0
tcoupl  = Berendsen
tc-grps = protein non-protein
tau-t   = 0.1 0.1
ref-t   = 298 298
nstxout = 1000
nstvout = 1000
nstxtcout   = 100
nstenergy   = 100

what can i do in order to get rid of this error.
your help is kindly needed. In case if i need to give more  information, 
please write back


There are two useful sources of information before posting questions:

1. The mailing list archive.
2. The wiki site (wiki.gromacs.org)

You will find a solution to this problem by searching the archive, as this 
question is frequently asked.  For further reading, have a look at:


http://wiki.gromacs.org/index.php/blowing_up

-Justin



shiny chandy





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--


Justin A. Lemkul
Graduate Research Assistant
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] Error in pdb2gmx

[vivek sharma]

Hi David,
Thanks for the quick reply. My apologies for asking you again a silly doubt
as, I am doing this all for the first time. It will be of great help if you
can tell me how to do such correction manually.

With Thanx,
Vivek

2008/8/12 David van der Spoel <[EMAIL PROTECTED]>

> vivek sharma wrote:
>
>> Hello there,
>> I am trying to run pdb2gmx on 3bzu.pdb file and got the following error
>>
>> Opening library file /usr/share/gromacs/top/
>> ffG43b1.rtp
>> Opening library file /usr/share/gromacs/top/aminoacids.dat
>> Reading 3bzu.pdb...
>> WARNING: all CONECT records are ignored
>> Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6 BETA-HSD1', 8581
>> atoms
>> Opening library file /usr/share/gromacs/top/xlateat.dat
>> 26 out of 26 lines of xlateat.dat converted succesfully
>> Analyzing pdb file
>>
>> ---
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: pdb2gmx.c, line: 878
>>
>> Fatal error:
>> Chain identifier 'A' was used in two non-sequential blocks (residue 1034,
>> atom 7961)
>> ---
>>  as I am new to this field. I'm finding it very difficult to find the
>> reason and rectify it.
>> Any suggestion would be of great help..
>>
> This is a limitation in pdb2gmx. It expects the atoms in the chain A to be
> in sequence in the pdb file. You can manually sort the pdb file on the chain
> identifier.
>
>
>> With Thanx,
>> Vivek
>> 
>>
>> ___
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Re: [gmx-users] Error in pdb2gmx

[David van der Spoel]

vivek sharma wrote:

Hi David,
Thanks for the quick reply. My apologies for asking you again a silly 
doubt as, I am doing this all for the first time. It will be of great 
help if you can tell me how to do such correction manually.


with a text editor, like emacs, notepad or whatever.


With Thanx,
Vivek

2008/8/12 David van der Spoel <[EMAIL PROTECTED] 
>


vivek sharma wrote:

Hello there,
I am trying to run pdb2gmx on 3bzu.pdb file and got the
following error

Opening library file /usr/share/gromacs/top/
ffG43b1.rtp
Opening library file /usr/share/gromacs/top/aminoacids.dat
Reading 3bzu.pdb...
WARNING: all CONECT records are ignored
Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
BETA-HSD1', 8581 atoms
Opening library file /usr/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file

---
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 878

Fatal error:
Chain identifier 'A' was used in two non-sequential blocks
(residue 1034, atom 7961)
---
 as I am new to this field. I'm finding it very difficult to
find the reason and rectify it.
Any suggestion would be of great help..

This is a limitation in pdb2gmx. It expects the atoms in the chain
A to be in sequence in the pdb file. You can manually sort the pdb
file on the chain identifier.


With Thanx,
Vivek


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[gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[vivek sharma]

Hi There,

I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the
command

 pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen
-water spce

I got the following in the last of error.
..
..
..
...
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom

---
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
---
 I tried the same with different force field and water models, but getting
the same error again and again.
any suggestion will be highly appreciated.


With thanx,
Vivek
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Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[David van der Spoel]

vivek sharma wrote:

Hi There,

I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the 
command


 pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite 
hydrogen -water spce


I got the following in the last of error.
..
..
..
...
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom

---
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
---
 I tried the same with different force field and water models, but 
getting the same error again and again.

any suggestion will be highly appreciated.


You have an incorrect pdb file. An atom is missing. You have to fix it 
yourself.



With thanx,
Vivek



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Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[Justin A. Lemkul]

vivek sharma wrote:

Hi There,

I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the 
command


 pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen 
-water spce


I got the following in the last of error.
..
..
..
...
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom

---
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
---
 I tried the same with different force field and water models, but 
getting the same error again and again.

any suggestion will be highly appreciated.



Sounds like the crystal structure has missing atoms.  You'll need to reconstruct 
the missing portions with a modeling program like DeepView or Modeller.


-Justin



With thanx,
Vivek




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--


Justin A. Lemkul
Graduate Research Assistant
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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[gmx-users] ASP-LIG Interaction Energy : MDRUN

[nahren manuel]

Dear Gromacs Users,
 
I have just completed one (5ns ) mdrun. 
 
Now If i want to calculate the interaction energy between two residues, my 
ligand and ASP104, how should I go about calculating the same.
 
The one option I know is by creating .ndx . But I did not expect this residue 
to play an important role when i started my simulation. So i did not include 
this protein residue ASP104 as a seperate group. 
 
Kindly advice.
 
regards,
nahren


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Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[vivek sharma]

Hi David,
Thanx a lot again. can you please tell me the criteria or the standards to
do such correction or can you suggest some link or tutorial for the same?
whether swiss pdb can help in such cases?

With Thanx,
Vivek



2008/8/12 David van der Spoel <[EMAIL PROTECTED]>

> vivek sharma wrote:
>
>> Hi There,
>>
>> I am new to molecular dynamics and GROMACS.
>> While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the
>> command
>>
>>  pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen
>> -water spce
>>
>> I got the following in the last of error.
>> ..
>> ..
>> ..
>> ...
>> N-terminus: NH3+
>> C-terminus: COO-
>> WARNING: atom CE2 not found in residue 270 while adding atom
>>
>> ---
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: genhydro.c, line: 304
>>
>> Fatal error:
>> Atom CE2 not found in residue PHE270 while adding hydrogens
>> ---
>>  I tried the same with different force field and water models, but getting
>> the same error again and again.
>> any suggestion will be highly appreciated.
>>
>
> You have an incorrect pdb file. An atom is missing. You have to fix it
> yourself.
>
>>
>>
>> With thanx,
>> Vivek
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>
>
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Re: [gmx-users] Error in pdb2gmx

[vivek sharma]

Hi david,
Thanx again, but I want to ask what changes need to be done there in such
cases.

With Thanx,
Vivek

2008/8/12 David van der Spoel <[EMAIL PROTECTED]>

> vivek sharma wrote:
>
>> Hi David,
>> Thanks for the quick reply. My apologies for asking you again a silly
>> doubt as, I am doing this all for the first time. It will be of great help
>> if you can tell me how to do such correction manually.
>>
>
> with a text editor, like emacs, notepad or whatever.
>
>>
>> With Thanx,
>> Vivek
>>
>> 2008/8/12 David van der Spoel <[EMAIL PROTECTED] > [EMAIL PROTECTED]>>
>>
>>
>>vivek sharma wrote:
>>
>>Hello there,
>>I am trying to run pdb2gmx on 3bzu.pdb file and got the
>>following error
>>
>>Opening library file /usr/share/gromacs/top/
>>ffG43b1.rtp
>>Opening library file /usr/share/gromacs/top/aminoacids.dat
>>Reading 3bzu.pdb...
>>WARNING: all CONECT records are ignored
>>Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
>>BETA-HSD1', 8581 atoms
>>Opening library file /usr/share/gromacs/top/xlateat.dat
>>26 out of 26 lines of xlateat.dat converted succesfully
>>Analyzing pdb file
>>
>>---
>>Program pdb2gmx, VERSION 3.3.3
>>Source code file: pdb2gmx.c, line: 878
>>
>>Fatal error:
>>Chain identifier 'A' was used in two non-sequential blocks
>>(residue 1034, atom 7961)
>>---
>> as I am new to this field. I'm finding it very difficult to
>>find the reason and rectify it.
>>Any suggestion would be of great help..
>>
>>This is a limitation in pdb2gmx. It expects the atoms in the chain
>>A to be in sequence in the pdb file. You can manually sort the pdb
>>file on the chain identifier.
>>
>>
>>With Thanx,
>>Vivek
>>
>>  
>>
>>___
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>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
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>>before posting!
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>>www interface or send it to [EMAIL PROTECTED]
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
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>>posting!
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>>
>> 
>>
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>
>
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Re: [gmx-users] Error in pdb2gmx

[Justin A. Lemkul]

vivek sharma wrote:

Hi david,
Thanx again, but I want to ask what changes need to be done there in 
such cases.




The chain identifier needs to be continuous.  That is, if you have atoms with 
chain identifiers like:


A
A
B
A
C
A
A

they should be re-written as:

A
A
A
A
A
B
C

This can be accomplished with some work in a simple text editor.

-Justin


With Thanx,
Vivek

2008/8/12 David van der Spoel <[EMAIL PROTECTED] 
>


vivek sharma wrote:

Hi David,
Thanks for the quick reply. My apologies for asking you again a
silly doubt as, I am doing this all for the first time. It will
be of great help if you can tell me how to do such correction
manually.


with a text editor, like emacs, notepad or whatever.


With Thanx,
Vivek

2008/8/12 David van der Spoel <[EMAIL PROTECTED]
 >>


   vivek sharma wrote:

   Hello there,
   I am trying to run pdb2gmx on 3bzu.pdb file and got the
   following error

   Opening library file /usr/share/gromacs/top/
   ffG43b1.rtp
   Opening library file /usr/share/gromacs/top/aminoacids.dat
   Reading 3bzu.pdb...
   WARNING: all CONECT records are ignored
   Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
   BETA-HSD1', 8581 atoms
   Opening library file /usr/share/gromacs/top/xlateat.dat
   26 out of 26 lines of xlateat.dat converted succesfully
   Analyzing pdb file

   ---
   Program pdb2gmx, VERSION 3.3.3
   Source code file: pdb2gmx.c, line: 878

   Fatal error:
   Chain identifier 'A' was used in two non-sequential blocks
   (residue 1034, atom 7961)
   ---
as I am new to this field. I'm finding it very difficult to
   find the reason and rectify it.
   Any suggestion would be of great help..

   This is a limitation in pdb2gmx. It expects the atoms in the
chain
   A to be in sequence in the pdb file. You can manually sort
the pdb
   file on the chain identifier.


   With Thanx,
   Vivek
 
 


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Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[Per Larsson]

If atoms are missing in the sidechains of your protein, you can try a  
program like scwrl3 to rebuild all or some of the sidechains. This  
will give you complete sidechains in sort of reasonable positions.


Cheers
/Per




12 aug 2008 kl. 15.04 skrev vivek sharma:


Hi David,
Thanx a lot again. can you please tell me the criteria or the  
standards to do such correction or can you suggest some link or  
tutorial for the same?

whether swiss pdb can help in such cases?

With Thanx,
Vivek



2008/8/12 David van der Spoel <[EMAIL PROTECTED]>
vivek sharma wrote:
Hi There,

I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using  
the command


 pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite  
hydrogen -water spce


I got the following in the last of error.
..
..
..
...
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom

---
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
---
 I tried the same with different force field and water models, but  
getting the same error again and again.

any suggestion will be highly appreciated.

You have an incorrect pdb file. An atom is missing. You have to fix  
it yourself.



With thanx,
Vivek



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Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[nahren manuel]

Dear Vivek,
you just have to download swisspdb and open your pdb file. Thats all you got to 
do and It is more than enough. If you have more than 2/3 residues missing then, 
make sure the Ramachandran plots are fine. Also try a simple minimization 
before begining gromacs.
 
nahren

--- On Tue, 8/12/08, vivek sharma <[EMAIL PROTECTED]> wrote:

From: vivek sharma <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue 
PHE270 while adding hydrogens
To: "Discussion list for GROMACS users" 
Date: Tuesday, August 12, 2008, 6:34 PM



Hi David,
Thanx a lot again. can you please tell me the criteria or the standards to do 
such correction or can you suggest some link or tutorial for the same?
whether swiss pdb can help in such cases?

With Thanx,
Vivek




2008/8/12 David van der Spoel <[EMAIL PROTECTED]>




vivek sharma wrote:

Hi There,

I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the 
command

 pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water 
spce

I got the following in the last of error.
...
...
...

N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom

---
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304

Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
---
 I tried the same with different force field and water models, but getting the 
same error again and again.
any suggestion will be highly appreciated.

You have an incorrect pdb file. An atom is missing. You have to fix it yourself.



With thanx,
Vivek



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Re: [gmx-users] ASP-LIG Interaction Energy : MDRUN

[Justin A. Lemkul]

nahren manuel wrote:

Dear Gromacs Users,
 
I have just completed one (5ns ) mdrun.
 
Now If i want to calculate the interaction energy between two residues, 
my ligand and ASP104, how should I go about calculating the same.
 
The one option I know is by creating .ndx . But I did not expect this 
residue to play an important role when i started my simulation. So i did 
not include this protein residue ASP104 as a seperate group.
 


What you're looking for is mdrun -rerun.  Make the appropriate index groups, and 
include them in your .mdp as energy-grps when creating a new .tpr file.  I think 
you will also need to set nstenergy = 1 in the new .mdp file for the re-run.


-Justin


Kindly advice.
 
regards,

nahren





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--


Justin A. Lemkul
Graduate Research Assistant
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] pdb2gmx -inter automatised ?

[Christian Fufezan]

Ok,

"pdb2gmx   < inter.txt" did the trick. Although it was a bit  
painful to generate the inter.txt in the first instance :)


Thanks again

Christian Fufezan


Dr. Christian Fufezan
Westfälische Wilhelms-Universität Münster
Institut für Biochemie und Biotechnologie der Pflanzen (IBBP)
Hindenburgplatz 55
48143 Münster - Germany

Tel: ++49 251 8324791
Fax: ++49 251 8328371
Web: http://www.fufezan.net

On Aug 11, 2008, at 20:33 , Justin A. Lemkul wrote:




Christian Fufezan wrote:

Dear gmx users,
I am new to MD and working my way through some tutorials. I saw  
that pdb2gmx has the "-inter" flag which is used to specify which  
conformers/protonation stats should be used.

Is there a way in which this can be automatised ?
For example, lets say I have a list.txt

HIS A 105 -> HISB

and I would like to use that list for all runs to be used.


Would this be useful:

http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive

Trying to automate this procedure using -inter is probably a lot  
more work than actually interacting with pdb2gmx.  If you're happy  
with the default protonation states of all the other titratable  
sites (check pdb2gmx -h), then you can use -his instead, which might  
de-complicate things.  Otherwise, you have to know the order of all  
the interactively selected residues, which protonation state to give  
them, and how many of each you have.


-Justin


Thanks in Advance
Christian Fufezan
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Justin A. Lemkul
Graduate Research Assistant
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] pdb2gmx -inter automatised ?

[Tsjerk Wassenaar]

Hi :)

Maybe these little scripts are useful...

The first, titratable.sh (use: titratable.sh file.pdb), generates a
list of residues for which the protonation state can be set, including
the termini. The second, gmxquery.sh (use: titratable.sh file.pdb |
gmxquery.sh) gives a series of 0 1 2, according to the protonation
states desired. So,

titratable.sh file.pdb | gmxquery.sh | pdb2gmx -f file.pdb -inter

should be close to what you want. The output from titratable.sh can
also be modified prior to piping it through gmxquery. And that can be
easily scripted :)

Do note that it doesn't deal with SS bonds.

Hope it helps,

Tsjerk

On Tue, Aug 12, 2008 at 3:26 PM, Christian Fufezan
<[EMAIL PROTECTED]> wrote:
> Ok,
>
> "pdb2gmx   < inter.txt" did the trick. Although it was a bit painful to
> generate the inter.txt in the first instance :)
>
> Thanks again
>
> Christian Fufezan
>
>
> Dr. Christian Fufezan
> Westfälische Wilhelms-Universität Münster
> Institut für Biochemie und Biotechnologie der Pflanzen (IBBP)
> Hindenburgplatz 55
> 48143 Münster - Germany
>
> Tel: ++49 251 8324791
> Fax: ++49 251 8328371
> Web: http://www.fufezan.net
>
> On Aug 11, 2008, at 20:33 , Justin A. Lemkul wrote:
>
>>
>>
>> Christian Fufezan wrote:
>>>
>>> Dear gmx users,
>>> I am new to MD and working my way through some tutorials. I saw that
>>> pdb2gmx has the "-inter" flag which is used to specify which
>>> conformers/protonation stats should be used.
>>> Is there a way in which this can be automatised ?
>>> For example, lets say I have a list.txt
>>> 
>>> HIS A 105 -> HISB
>>> 
>>> and I would like to use that list for all runs to be used.
>>
>> Would this be useful:
>>
>> http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive
>>
>> Trying to automate this procedure using -inter is probably a lot more work
>> than actually interacting with pdb2gmx.  If you're happy with the default
>> protonation states of all the other titratable sites (check pdb2gmx -h),
>> then you can use -his instead, which might de-complicate things.  Otherwise,
>> you have to know the order of all the interactively selected residues, which
>> protonation state to give them, and how many of each you have.
>>
>> -Justin
>>
>>> Thanks in Advance
>>> Christian Fufezan
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
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>>> interface or send it to [EMAIL PROTECTED]
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>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623


titratable.sh
Description: Bourne shell script


gmxquery.sh
Description: Bourne shell script
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[gmx-users] Re: requested for GROMACS package

[Vitaly Chaban]

> hello
> I am working with protien 1PGB having 56 amino acids (practical tutorial
> from GROMACS web site) for its simulation using the flexilbe water.
> the commands that i have run are :
>
> At later stsges of MD simulations ( i.e after position restrained MD), I
> have been getting few errors which are as follow:
> ---
> *./grompp –f run.mdp –p topol.top –c pr.gro –o run.tpr*
>  followed by
> *./mdrun –v –deffnm run*
> 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.

You're just exploding. Try energy minimization (integrator=l_bfgs)
before running MD.

Obviously, you missed some stage of the example or it did not finish
correctly. You can also run the example from beginning carefully.


P.S. Justin is extremely strict today. :)


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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Re: [gmx-users] Error in pdb2gmx

[Tsjerk Wassenaar]

Well,

sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- > sorted.pdb

sort of seems to do the trick. But it will place the chainless things first.

Hope it helps,

Tsjerk

On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> vivek sharma wrote:
>>
>> Hi david,
>> Thanx again, but I want to ask what changes need to be done there in such
>> cases.
>>
>
> The chain identifier needs to be continuous.  That is, if you have atoms
> with chain identifiers like:
>
> A
> A
> B
> A
> C
> A
> A
>
> they should be re-written as:
>
> A
> A
> A
> A
> A
> B
> C
>
> This can be accomplished with some work in a simple text editor.
>
> -Justin
>
>> With Thanx,
>> Vivek
>>
>> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>> >
>>
>>vivek sharma wrote:
>>
>>Hi David,
>>Thanks for the quick reply. My apologies for asking you again a
>>silly doubt as, I am doing this all for the first time. It will
>>be of great help if you can tell me how to do such correction
>>manually.
>>
>>
>>with a text editor, like emacs, notepad or whatever.
>>
>>
>>With Thanx,
>>Vivek
>>
>>2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>> >>>
>>
>>
>>   vivek sharma wrote:
>>
>>   Hello there,
>>   I am trying to run pdb2gmx on 3bzu.pdb file and got the
>>   following error
>>
>>   Opening library file /usr/share/gromacs/top/
>>   ffG43b1.rtp
>>   Opening library file /usr/share/gromacs/top/aminoacids.dat
>>   Reading 3bzu.pdb...
>>   WARNING: all CONECT records are ignored
>>   Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
>>   BETA-HSD1', 8581 atoms
>>   Opening library file /usr/share/gromacs/top/xlateat.dat
>>   26 out of 26 lines of xlateat.dat converted succesfully
>>   Analyzing pdb file
>>
>>   ---
>>   Program pdb2gmx, VERSION 3.3.3
>>   Source code file: pdb2gmx.c, line: 878
>>
>>   Fatal error:
>>   Chain identifier 'A' was used in two non-sequential blocks
>>   (residue 1034, atom 7961)
>>   ---
>>as I am new to this field. I'm finding it very difficult to
>>   find the reason and rectify it.
>>   Any suggestion would be of great help..
>>
>>   This is a limitation in pdb2gmx. It expects the atoms in the
>>chain
>>   A to be in sequence in the pdb file. You can manually sort
>>the pdb
>>   file on the chain identifier.
>>
>>
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[gmx-users] one component plasma simulations (OCP)

[Argyrios Karatrantos]

hi, 
is it possible to do one component plasma (OCP) simulations using gromacs?
in the one component plasma (OCP) charged particles immersed into a homogeneous
neutralizing backround. 
so i would guess that the neutralizing backround is the difficult thing for 
gromacs
i would appreciate very much if you have any idea of how to do this in gromacs
thanks very much


  
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Re: [gmx-users] one component plasma simulations (OCP)

[David van der Spoel]

Argyrios Karatrantos wrote:
hi, 
is it possible to do one component plasma (OCP) simulations using gromacs?

in the one component plasma (OCP) charged particles immersed into a homogeneous
neutralizing backround. 
so i would guess that the neutralizing backround is the difficult thing for gromacs

i would appreciate very much if you have any idea of how to do this in gromacs
thanks very much
  
What does that mean? Charged particles with screened Coulomb? The PME 
algorithm will compensate for a net charge by a neutralizing background 
charge. You may also want to check this ref (Phys Rev E *70* pp. 051904 
(*2004*), http://folding.bmc.uu.se/david/oldpapers/bergh2004a.pdf) where 
we used an inhomogenous electron plasma. This was done in GROMACS but in 
a modified version.





  
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[gmx-users] gmx does not recognize HIE as protein

[Rebeca García Fandiño]

Hello,
I am trying to simulate a protein that has 2 chains (in a membrane, but the 
problem is in the protein). One of the chains of the protein has 416 residues 
and the other 421. I want to simulate it using the amber force field, so I have 
prepared the topology for each one of them and then converted them with 
amb2gmx.pl.
 
When I do grompp of the complete system I can see that it is only considering 
821 residues of the protein, and they should be 837!!:
 
Opening library file 
/gpfs/projects/ub51/ub51077/GROMACS-4.0-DEV/share/gromacs/top/aminoacids.datThere
 are: 157455  OTHER residuesThere are:   821PROTEIN residuesThere are:  
   0DNA residues
 
The problem is that the program considers residues HIE out of the protein 
(histidines):
 
  0 System  : 716705 atoms  1 Protein : 12658 atoms  2 
Protein-H   :  6344 atoms  3 C-alpha :   821 atoms  4 
Backbone:  2463 atoms  5 MainChain   :  3286 atoms  6 
MainChain+Cb:  4038 atoms  7 MainChain+H :  4072 atoms  8 
SideChain   :  8586 atoms  9 SideChain-H :  3058 atoms 10 
Prot-Masses : 12658 atoms 11 Non-Protein : 704047 atoms 12 HIE  
   :   272 atoms 13 dop : 238464 atoms 14 SOL   
  : 464400 atoms 15 Na  :   467 atoms 16 Cl 
 :   444 atoms 17 Other   : 704047 atoms
 
I have tried to use both chains together and repeating the same, but the result 
is the same.
 
What could I do? Anybody knows why there is a problem with HIE?
 
Thank you very much in advance,
 
Rebeca Garcia Fandiño
Parc Cientific de Barcelona
 
 
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Re: [gmx-users] gmx does not recognize HIE as protein

[Tsjerk Wassenaar]

Hi Rebeca,

In the GMX data directory ($GMXDATA) there's a file aminoacids.dat
listing what should be recognized as amino acids. Either edit the file
and add HIE (also incrementing the counter at the top line) or make a
local copy of the file in the directory where you need it and edit
that.

Cheers,

Tsjerk

On Tue, Aug 12, 2008 at 5:47 PM, Rebeca García Fandiño
<[EMAIL PROTECTED]> wrote:
> Hello,
> I am trying to simulate a protein that has 2 chains (in a membrane, but the
> problem is in the protein). One of the chains of the protein has 416
> residues and the other 421. I want to simulate it using the amber force
> field, so I have prepared the topology for each one of them and then
> converted them with amb2gmx.pl.
>
> When I do grompp of the complete system I can see that it is only
> considering 821 residues of the protein, and they should be 837!!:
>
> Opening library file
> /gpfs/projects/ub51/ub51077/GROMACS-4.0-DEV/share/gromacs/top/aminoacids.dat
> There are: 157455  OTHER residues
> There are:   821PROTEIN residues
> There are: 0DNA residues
>
> The problem is that the program considers residues HIE out of the protein
> (histidines):
>
>   0 System  : 716705 atoms
>   1 Protein : 12658 atoms
>   2 Protein-H   :  6344 atoms
>   3 C-alpha :   821 atoms
>   4 Backbone:  2463 atoms
>   5 MainChain   :  3286 atoms
>   6 MainChain+Cb:  4038 atoms
>   7 MainChain+H :  4072 atoms
>   8 SideChain   :  8586 atoms
>   9 SideChain-H :  3058 atoms
>  10 Prot-Masses : 12658 atoms
>  11 Non-Protein : 704047 atoms
>  12 HIE :   272 atoms
>  13 dop : 238464 atoms
>  14 SOL : 464400 atoms
>  15 Na  :   467 atoms
>  16 Cl  :   444 atoms
>  17 Other   : 704047 atoms
>
>
> I have tried to use both chains together and repeating the same, but the
> result is the same.
>
> What could I do? Anybody knows why there is a problem with HIE?
>
> Thank you very much in advance,
>
> Rebeca Garcia Fandiño
> Parc Cientific de Barcelona
>
>
>
>
> 
> ¡Es tiempo de inaugurar tu piscina! Entra en Eventos e invita a todos tus
> amigos, crea paneles de discusión y sube las fotos más divertidas Eventos
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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] debian packages from CVS versions

[Martin Höfling]

Hi Folks,

JFYI, I packaged the cvs version for deb based distributions (ubuntu, 
debian... ). I can provide source packages to build, update (from cvs) and 
install the current and probably future cvs versions on your machines.

The packages should be installable together with 3.x packages since they're 
using a 4 as suffix, e.g. mdrun4 or mdrun4_mpi etc.

If your're interested in testing, send me a email.

Best wishes
Martin

Hint: You should know how to compile binary packages from a source package on 
deb based distributions.
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[gmx-users] error: 1 particles communicated to PME node 3 (...)

[Rebeca García Fandiño]

Hello,
I am trying to equilibrate a protein+membrane system in Gromacs 4. The 
minimization went OK, but in the equilibration at constant pressure I got this 
error:
 
 
Fatal error:1 particles communicated to PME node 3 are more than a cell length 
out of the domain decomposition cell of their charge 
group---
"O My God, They Killed Kenny !" (South Park)
Error on node 15, will try to stop all the nodesHalting parallel program 
mdrun_mpi on CPU 15 out of 32
gcq#254: "O My God, They Killed Kenny !" (South Park)
[15] MPI Abort by user Aborting program !mx_finalize() called while some 
endpoints are still open.MX:s23c2b13:mx_finalize:error 20(errno=2):Busysrun: 
error: s23c2b13: task15: Exited with exit code 1MX:s23c2b06:Remote endpoint is 
closed, peer=00:60:dd:48:46:62 (s23c2b13:0)srun: error: s23c2b06: task11: 
Exited with exit code 1srun: error: s23c2b13: task[12-14]: Killedsrun: Job 
Failed
 
The calculations stops after 2000 steps:
 
   Step   Time Lambda   20004.0 
   0.0
   Energies (kJ/mol)  Angle Ryckaert-Bell.  LJ-14 
Coulomb-14LJ (SR)6.17238e+054.06472e+051.89810e+05
5.82538e+053.71263e+06LJ (LR)   Coulomb (SR)   Coul. recip. 
Position Rest.  Potential   -5.12910e+04   -9.09326e+06   -1.97121e+06
1.69698e+06   -3.91010e+06Kinetic En.   Total EnergyTemperature 
Pressure (bar)  Cons. rmsd ()2.12885e+06   -1.78125e+063.56627e+02   
-2.35301e+042.99204e-05
 
As input I use:
 
title   = EQUILIBRADOcpp = /usr/bin/cppinclude = 
-I../topdefine  = -DPOSRES_D -DPOSRES_Pconstraints = 
all-bondsintegrator  = mddt  = 0.002nsteps  = 
1nstxout = 1000nstvout = 1000nstlog  = 
1000nstenergy   = 1000nstxtcout   = 1000nstlist = 10ns_type 
= gridrlist   = 1.0coulombtype = PMErcoulomb= 
1.0vdwtype = cut-offrvdw= 1.4pme_order   = 4ewald_rtol  
= 1e-5optimize_fft= yes;Berendsen temperature coupling is onTcoupl  
= berendsentau_t   = 0.1 0.10.1tc-grps = Protein 
dop SOL_Na_Clref_t   = 310 310310; Pressure couplingPcoupl  
 = Parrinello-RahmanPcoupltype   = Semiisotropic; Time 
constant (ps), compressibility (1/bar) and reference P (bar)tau-p   
 = 1.0 1.0compressibility  = 4.6E-5 4.6E-5ref-p
= 1.0 1.0;Generate velocities is on at 310 Kgen_vel = yesgen_temp   
 = 310gen_seed= 173529
Does anybody which could be the problem?
 
Thank you very much for your help.
 
Best wishes,
 
Rebeca Garcia Fandiño
Parc Cientific de Barcelona
 
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Re: [gmx-users] error: 1 particles communicated to PME node 3 (...)

[Justin A. Lemkul]

Which version of CVS are you using?  (This sounds like a question for the 
gmx-developers listserv.)  I believe this problem was fixed in CVS over a month ago:


http://www.gromacs.org/pipermail/gmx-developers/2008-July/002608.html

Although there is a possibility that something is really wrong, which Berk 
mentions in that post.


-Justin

Rebeca García Fandiño wrote:

Hello,
I am trying to equilibrate a protein+membrane system in Gromacs 4. The 
minimization went OK, but in the equilibration at constant pressure I 
got this error:
 
 
Fatal error:
1 particles communicated to PME node 3 are more than a cell length out 
of the domain decomposition cell of their charge group

---
"O My God, They Killed Kenny !" (South Park)
Error on node 15, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 15 out of 32
gcq#254: "O My God, They Killed Kenny !" (South Park)
[15] MPI Abort by user Aborting program !
mx_finalize() called while some endpoints are still open.
MX:s23c2b13:mx_finalize:error 20(errno=2):Busy
srun: error: s23c2b13: task15: Exited with exit code 1
MX:s23c2b06:Remote endpoint is closed, peer=00:60:dd:48:46:62 (s23c2b13:0)
srun: error: s23c2b06: task11: Exited with exit code 1
srun: error: s23c2b13: task[12-14]: Killed
srun: Job Failed
 
The calculations stops after 2000 steps:
 
   Step   Time Lambda

   20004.00.0
   Energies (kJ/mol)
  Angle Ryckaert-Bell.  LJ-14 Coulomb-14LJ (SR)
6.17238e+054.06472e+051.89810e+055.82538e+053.71263e+06
LJ (LR)   Coulomb (SR)   Coul. recip. Position Rest.  Potential
   -5.12910e+04   -9.09326e+06   -1.97121e+061.69698e+06   -3.91010e+06
Kinetic En.   Total EnergyTemperature Pressure (bar)  Cons. rmsd ()
2.12885e+06   -1.78125e+063.56627e+02   -2.35301e+042.99204e-05
 
As input I use:
 
title   = EQUILIBRADO

cpp = /usr/bin/cpp
include = -I../top
define  = -DPOSRES_D -DPOSRES_P
constraints = all-bonds
integrator  = md
dt  = 0.002
nsteps  = 1
nstxout = 1000
nstvout = 1000
nstlog  = 1000
nstenergy   = 1000
nstxtcout   = 1000
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
;Berendsen temperature coupling is on
Tcoupl  = berendsen
tau_t   = 0.1 0.10.1
tc-grps = Protein dop SOL_Na_Cl
ref_t   = 310 310310
; Pressure coupling
Pcoupl   = Parrinello-Rahman
Pcoupltype   = Semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1.0 1.0
compressibility  = 4.6E-5 4.6E-5
ref-p= 1.0 1.0
;Generate velocities is on at 310 K
gen_vel = yes
gen_temp= 310
gen_seed= 173529

Does anybody which could be the problem?
 
Thank you very much for your help.
 
Best wishes,
 
Rebeca Garcia Fandiño

Parc Cientific de Barcelona


 



¡Es tiempo de inaugurar tu piscina! Entra en Eventos e invita a todos 
tus amigos, crea paneles de discusión y sube las fotos más divertidas 
Eventos 





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Justin A. Lemkul
Graduate Research Assistant
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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[gmx-users] Force Field Parameters Nitrogen and Oxygen

[Andy Shelley]

I am trying to simulate air and have not been able to find force field
parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond.  If you could
please direct me to where these could be found I would appreciate it.

Thanks,
Andy
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[gmx-users] OCP simulations

[Argyrios Karatrantos]

hi David 
A one-component plasma (OCP) is a system in which a single species of charged 
particle
moves in a uniform backround of the opposite charge.  Systems of this nature 
exist in the dense stellar matter of white-dwarf stars.
when the screening parameter of the screened Coulomb goes to zero then we have 
the Coulombic one-component plasma
you are right , in gromacs 3.3.1 , it is possible to use a uniform neutralizing 
backround in PME to  compensate for a system with a net backround charge. it is 
not necessary to add counterions to neutralize the system.
thank you very much



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Re: [gmx-users] Force Field Parameters Nitrogen and Oxygen

[Justin A. Lemkul]

Andy Shelley wrote:
I am trying to simulate air and have not been able to find force field 
parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond.  If you 
could please direct me to where these could be found I would appreciate it.




I believe these values typically come from spectroscopic measurements.

-Justin


Thanks,
Andy




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Justin A. Lemkul
Graduate Research Assistant
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] Re: requested for GROMACS package

[Justin A. Lemkul]

Vitaly Chaban wrote:



P.S. Justin is extremely strict today. :)



Apologies if I've been coming of a bit dry or sarcastic.  I do try to help, at 
least by pointing individuals to the proper resources.  We seem to be getting 
the same questions day after day :)  I myself have received quite a bit of help 
from generous individuals.


My motto is, "Teach a man to fish, and he'll be satisfied for life, but if you 
simply give him the fish, he'll ask you the next day why his fish gave a 
segmentation fault."


-Justin






--


Justin A. Lemkul
Graduate Research Assistant
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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[gmx-users] A bug of trjconv for force output?

[LuLanyuan]

Hello All,
I just found a strange problem for the gromacs tool trjconv. I have a 
trajectory (and the tpr file) which contains three groups of molecules and x,v 
and f. When I use trjconv to output the trajectory of the 1st group, everything 
is fine. For example, I have A,B and C groups in my trajectory and I choose A 
only at the prompt of trjconv and use "-force" option to include forces in my 
output trajectory of A only. But if I want a trajectory of C only, I found the 
output forces were wrong. Positions and velocities are right in this case. It 
seems to me the trjconv just pick the first N force numbers to write where N is 
the total number of atoms in group C. In fact these forces belong to group A 
and B. This "logic" of trjconv explains why the output is correct if I choose 
the first group A to write.
Some month ago I reported a problem regarding the deshuf.ndx and the wrong 
force output. I think that problem is related to this problem. Because fewer 
people use forces, I think this is the reason these bugs haven't been found 
before. I appreciate if some authors can fix them.
Thanks.
Lanyuan Lu 
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[gmx-users] colour of the molecules

[hhhh huan]

Dear all gmx-users and developers,

There are 6 different type of molecules in my simulation system. So how can I 
differentiate o recognize the type of those molecules? which files (topology, 
trr or others) should I look at? 

Any suggestions are appreciated.
Thanks



  
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Re: [gmx-users] Error in pdb2gmx

[vivek sharma]

Thanx David and Tsjerk,
  I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
sorted  pdb file was giving the following error.
Sorting it all out...
Opening library file /usr/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
Processing chain 1 'A' (2108 atoms, 601 residues)
There are 393 donors and 383 acceptors
There are 533 hydrogen bonds

---
Program pdb2gmx, VERSION 3.3.3
Source code file: hizzie.c, line: 267

Fatal error:
Incomplete ring in HIS194
---

Here I am attaching the sorted.pdb file, it is having some amino acids
inserted between some other amino acid as below
text from sorted pdb shows GLN and GLU are inserted in HIS

ATOM793  CD2 PHE A 129  -1.911  -9.897   3.599  1.00 43.21
C
ATOM794  CE1 PHE A 129  -1.839 -11.242   5.997  1.00 41.19
C
ATOM795  CE2 PHE A 129  -2.911 -10.794   3.911  1.00 41.19
C
ATOM796  CZ  PHE A 129  -2.874 -11.465   5.104  1.00 42.09
C
ATOM797  N   HIS A 130   1.739 -11.572   3.175  1.00 54.14
N
ATOM798  CA  HIS A 130   1.520 -12.688   2.246  1.00 55.63
C
ATOM799  C   HIS A 130   0.177 -13.421   2.474  1.00 55.34
C
ATOM 79  CD  GLN A  33   8.099  10.312  47.238  1.00 69.55
C
ATOM  7  CD  GLU A  25  -0.646  19.004  39.566  1.00 87.49
C
ATOM800  O   HIS A 130  -0.859 -13.049   1.913  1.00 56.40
O
ATOM801  CB  HIS A 130   2.726 -13.659   2.201  1.00 56.33
C
ATOM802  CG  HIS A 130   3.542 -13.730   3.467  1.00 58.59
C
ATOM803  ND1 HIS A 130   4.249 -12.655   3.970  1.00 60.95
N
ATOM804  CD2 HIS A 130   3.828 -14.777   4.284  1.00 59.58
C
ATOM805  CE1 HIS A 130   4.895 -13.022   5.066  1.00 60.24
C
ATOM806  NE2 HIS A 130   4.657 -14.305   5.279  1.00 60.16
N
ATOM807  N   ASP A 131   0.207 -14.462   3.285  1.00 54.76
N
ATOM808  CA  ASP A 131  -0.954 -15.320   3.512  1.00 54.01
C
ATOM809  C   ASP A 131  -1.040 -15.548   4.997  1.00 51.90
C
ATOM 80  OE1 GLN A  33   7.692  11.421  46.868  1.00 70.33
O

Kindly suggest any way to correct the .pdb file so that it can be converted
to .gro file

With Thanx,
Vivek


2008/8/12 Tsjerk Wassenaar <[EMAIL PROTECTED]>

> Well,
>
> sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
> file.pdb | sort | cut -b 2- > sorted.pdb
>
> sort of seems to do the trick. But it will place the chainless things
> first.
>
> Hope it helps,
>
> Tsjerk
>
> On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> >
> >
> > vivek sharma wrote:
> >>
> >> Hi david,
> >> Thanx again, but I want to ask what changes need to be done there in
> such
> >> cases.
> >>
> >
> > The chain identifier needs to be continuous.  That is, if you have atoms
> > with chain identifiers like:
> >
> > A
> > A
> > B
> > A
> > C
> > A
> > A
> >
> > they should be re-written as:
> >
> > A
> > A
> > A
> > A
> > A
> > B
> > C
> >
> > This can be accomplished with some work in a simple text editor.
> >
> > -Justin
> >
> >> With Thanx,
> >> Vivek
> >>
> >> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]
> >> >
> >>
> >>vivek sharma wrote:
> >>
> >>Hi David,
> >>Thanks for the quick reply. My apologies for asking you again a
> >>silly doubt as, I am doing this all for the first time. It will
> >>be of great help if you can tell me how to do such correction
> >>manually.
> >>
> >>
> >>with a text editor, like emacs, notepad or whatever.
> >>
> >>
> >>With Thanx,
> >>Vivek
> >>
> >>2008/8/12 David van der Spoel <[EMAIL PROTECTED]
> >>  >>>>
> >>
> >>
> >>   vivek sharma wrote:
> >>
> >>   Hello there,
> >>   I am trying to run pdb2gmx on 3bzu.pdb file and got the
> >>   following error
> >>
> >>   Opening library file /usr/share/gromacs/top/
> >>   ffG43b1.rtp
> >>   Opening library file /usr/share/gromacs/top/aminoacids.dat
> >>   Reading 3bzu.pdb...
> >>   WARNING: all CONECT records are ignored
> >>   Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
> >>   BETA-HSD1', 8581 atoms
> >>   Opening library file /usr/share/gromacs/top/xlateat.dat
> >>   26 out of 26 lines of xlateat.dat converted succesfully
> >>   Analyzing pdb file
> >>
> >>   ---
> >>   Program pdb2gmx, VERSION 3.3.3
> >>   Source code file: pdb2gmx.c, line: 878
> >>
> >>   Fatal error:
> >>   Chain identifier 'A' was used in two non-sequential

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

[vivek sharma]

Hi Nahren,
Thanx for your help, I opened the pdb file with swisspdb viewer and then
tried the pdb2gmx command over that pdb file and got the following error.

Total mass 28295.072 a.m.u.
Total charge 1.000 e
Writing topology
Processing chain 5 'E' (372 atoms, 9 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: 'NDP' not found in residue topology database, trying to use 'NDPH'

---
Program pdb2gmx, VERSION 3.3.3
Source code file: pdb2gmx.c, line: 421

Fatal error:
Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms
 while sorting atoms
---

and the error for the all atom forcefield were as follow.

---
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 436

Fatal error:
Residue 'NDP' not found in residue topology database

---


any advice for this will be of great help for me.

Thanx,
Vivek

2008/8/12 nahren manuel <[EMAIL PROTECTED]>

> Dear Vivek,
> you just have to download swisspdb and open your pdb file. Thats all you
> got to do and It is more than enough. If you have more than 2/3 residues
> missing then, make sure the Ramachandran plots are fine. Also try a simple
> minimization before begining gromacs.
>
> nahren
>
> --- On *Tue, 8/12/08, vivek sharma <[EMAIL PROTECTED]>* wrote:
>
> From: vivek sharma <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue
> PHE270 while adding hydrogens
> To: "Discussion list for GROMACS users" 
> Date: Tuesday, August 12, 2008, 6:34 PM
>
>
>  Hi David,
> Thanx a lot again. can you please tell me the criteria or the standards to
> do such correction or can you suggest some link or tutorial for the same?
> whether swiss pdb can help in such cases?
>
> With Thanx,
> Vivek
>
>
>
> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]>
>
>>  vivek sharma wrote:
>>
>>> Hi There,
>>>
>>> I am new to molecular dynamics and GROMACS.
>>> While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the
>>> command
>>>
>>>  pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen
>>> -water spce
>>>
>>> I got the following in the last of error.
>>> ..
>>> ..
>>> ..
>>> ...
>>> N-terminus: NH3+
>>> C-terminus: COO-
>>> WARNING: atom CE2 not found in residue 270 while adding atom
>>>
>>> ---
>>> Program pdb2gmx, VERSION 3.3.3
>>> Source code file: genhydro.c, line: 304
>>>
>>> Fatal error:
>>> Atom CE2 not found in residue PHE270 while adding hydrogens
>>> ---
>>>  I tried the same with different force field and water models, but
>>> getting the same error again and again.
>>> any suggestion will be highly appreciated.
>>>
>>
>> You have an incorrect pdb file. An atom is missing. You have to fix it
>> yourself.
>>
>>>
>>>
>>> With thanx,
>>> Vivek
>>>
>>> 
>>>
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
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>>>
>>
>>
>> ___
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>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>
> ___
> gmx-users mailing list[EMAIL 
> PROTECTED]://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
>
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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Please sea

Re: [gmx-users] Error in pdb2gmx

[Tsjerk Wassenaar]

Hi Vivek,

Sorry, I should've been more careful. Sorting will obviously take the
rest of the line in account. I'll send a proper solution in a few
moments...

Cheers,

Tsjerk

On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma
<[EMAIL PROTECTED]> wrote:
> Thanx David and Tsjerk,
>   I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
> sorted  pdb file was giving the following error.
> Sorting it all out...
> Opening library file /usr/share/gromacs/top/
> ffG43a1.hdb
> Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
> Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
> Processing chain 1 'A' (2108 atoms, 601 residues)
> There are 393 donors and 383 acceptors
> There are 533 hydrogen bonds
>
> ---
> Program pdb2gmx, VERSION 3.3.3
> Source code file: hizzie.c, line: 267
>
> Fatal error:
> Incomplete ring in HIS194
> ---
>
> Here I am attaching the sorted.pdb file, it is having some amino acids
> inserted between some other amino acid as below
> text from sorted pdb shows GLN and GLU are inserted in HIS
>
> ATOM793  CD2 PHE A 129  -1.911  -9.897   3.599  1.00 43.21
> C
> ATOM794  CE1 PHE A 129  -1.839 -11.242   5.997  1.00 41.19
> C
> ATOM795  CE2 PHE A 129  -2.911 -10.794   3.911  1.00 41.19
> C
> ATOM796  CZ  PHE A 129  -2.874 -11.465   5.104  1.00 42.09
> C
> ATOM797  N   HIS A 130   1.739 -11.572   3.175  1.00 54.14
> N
> ATOM798  CA  HIS A 130   1.520 -12.688   2.246  1.00 55.63
> C
> ATOM799  C   HIS A 130   0.177 -13.421   2.474  1.00 55.34
> C
> ATOM 79  CD  GLN A  33   8.099  10.312  47.238  1.00 69.55
> C
> ATOM  7  CD  GLU A  25  -0.646  19.004  39.566  1.00 87.49
> C
> ATOM800  O   HIS A 130  -0.859 -13.049   1.913  1.00 56.40
> O
> ATOM801  CB  HIS A 130   2.726 -13.659   2.201  1.00 56.33
> C
> ATOM802  CG  HIS A 130   3.542 -13.730   3.467  1.00 58.59
> C
> ATOM803  ND1 HIS A 130   4.249 -12.655   3.970  1.00 60.95
> N
> ATOM804  CD2 HIS A 130   3.828 -14.777   4.284  1.00 59.58
> C
> ATOM805  CE1 HIS A 130   4.895 -13.022   5.066  1.00 60.24
> C
> ATOM806  NE2 HIS A 130   4.657 -14.305   5.279  1.00 60.16
> N
> ATOM807  N   ASP A 131   0.207 -14.462   3.285  1.00 54.76
> N
> ATOM808  CA  ASP A 131  -0.954 -15.320   3.512  1.00 54.01
> C
> ATOM809  C   ASP A 131  -1.040 -15.548   4.997  1.00 51.90
> C
> ATOM 80  OE1 GLN A  33   7.692  11.421  46.868  1.00 70.33
> O
>
> Kindly suggest any way to correct the .pdb file so that it can be converted
> to .gro file
>
> With Thanx,
> Vivek
>
> 2008/8/12 Tsjerk Wassenaar <[EMAIL PROTECTED]>
>>
>> Well,
>>
>> sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
>> file.pdb | sort | cut -b 2- > sorted.pdb
>>
>> sort of seems to do the trick. But it will place the chainless things
>> first.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>> >
>> >
>> > vivek sharma wrote:
>> >>
>> >> Hi david,
>> >> Thanx again, but I want to ask what changes need to be done there in
>> >> such
>> >> cases.
>> >>
>> >
>> > The chain identifier needs to be continuous.  That is, if you have atoms
>> > with chain identifiers like:
>> >
>> > A
>> > A
>> > B
>> > A
>> > C
>> > A
>> > A
>> >
>> > they should be re-written as:
>> >
>> > A
>> > A
>> > A
>> > A
>> > A
>> > B
>> > C
>> >
>> > This can be accomplished with some work in a simple text editor.
>> >
>> > -Justin
>> >
>> >> With Thanx,
>> >> Vivek
>> >>
>> >> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>> >> >
>> >>
>> >>vivek sharma wrote:
>> >>
>> >>Hi David,
>> >>Thanks for the quick reply. My apologies for asking you again a
>> >>silly doubt as, I am doing this all for the first time. It will
>> >>be of great help if you can tell me how to do such correction
>> >>manually.
>> >>
>> >>
>> >>with a text editor, like emacs, notepad or whatever.
>> >>
>> >>
>> >>With Thanx,
>> >>Vivek
>> >>
>> >>2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>> >> > >>>>
>> >>
>> >>
>> >>   vivek sharma wrote:
>> >>
>> >>   Hello there,
>> >>   I am trying to run pdb2gmx on 3bzu.pdb file and got the
>> >>   following error
>> >>
>> >>   Opening library file /usr/share/gromacs/top/
>> >>   ffG43b1.rtp
>> >>   Opening library file
>> >> /usr/share/gromacs/top/aminoacids.dat
>> >>   Reading 3bzu.pdb...
>> >>   WARNING: all CONECT records are ignored
>> >>   Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
>> >>   BETA-HSD1', 8581 atoms

Re: [gmx-users] Error in pdb2gmx

[Tsjerk Wassenaar]

Hi Vivek,

I downloaded 3bzu.pdb and ran the sorting on it as I described before
(sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
3bzu.pdb | sort | cut -b 2-), and it worked perfectly for me. I don't
see how you'd end up with some atoms inbetween other residues. It
seems as if the sorting counts space > number.
I do see another problem though, which is more fundamental to your
initial problem. The resason for not having consecutive chain
identifiers is that all hetatms are placed at the end of the atom
listing. If these hetatm residues are part of the same molecule, you'd
be on the right route (sorting and running pdb2gmx), but you'll have
to make sure you have building block descriptions. If these are not
part of the same molecule, you better remove them from the file before
running pdb2gmx, make topology include files for each separate
molecule and combine these later on. If you don't understand what I'm
talking about, don't do it; pick another protein.

Cheers,

Tsjerk

On Wed, Aug 13, 2008 at 7:37 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Vivek,
>
> Sorry, I should've been more careful. Sorting will obviously take the
> rest of the line in account. I'll send a proper solution in a few
> moments...
>
> Cheers,
>
> Tsjerk
>
> On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma
> <[EMAIL PROTECTED]> wrote:
>> Thanx David and Tsjerk,
>>   I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
>> sorted  pdb file was giving the following error.
>> Sorting it all out...
>> Opening library file /usr/share/gromacs/top/
>> ffG43a1.hdb
>> Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
>> Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
>> Processing chain 1 'A' (2108 atoms, 601 residues)
>> There are 393 donors and 383 acceptors
>> There are 533 hydrogen bonds
>>
>> ---
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: hizzie.c, line: 267
>>
>> Fatal error:
>> Incomplete ring in HIS194
>> ---
>>
>> Here I am attaching the sorted.pdb file, it is having some amino acids
>> inserted between some other amino acid as below
>> text from sorted pdb shows GLN and GLU are inserted in HIS
>>
>> ATOM793  CD2 PHE A 129  -1.911  -9.897   3.599  1.00 43.21
>> C
>> ATOM794  CE1 PHE A 129  -1.839 -11.242   5.997  1.00 41.19
>> C
>> ATOM795  CE2 PHE A 129  -2.911 -10.794   3.911  1.00 41.19
>> C
>> ATOM796  CZ  PHE A 129  -2.874 -11.465   5.104  1.00 42.09
>> C
>> ATOM797  N   HIS A 130   1.739 -11.572   3.175  1.00 54.14
>> N
>> ATOM798  CA  HIS A 130   1.520 -12.688   2.246  1.00 55.63
>> C
>> ATOM799  C   HIS A 130   0.177 -13.421   2.474  1.00 55.34
>> C
>> ATOM 79  CD  GLN A  33   8.099  10.312  47.238  1.00 69.55
>> C
>> ATOM  7  CD  GLU A  25  -0.646  19.004  39.566  1.00 87.49
>> C
>> ATOM800  O   HIS A 130  -0.859 -13.049   1.913  1.00 56.40
>> O
>> ATOM801  CB  HIS A 130   2.726 -13.659   2.201  1.00 56.33
>> C
>> ATOM802  CG  HIS A 130   3.542 -13.730   3.467  1.00 58.59
>> C
>> ATOM803  ND1 HIS A 130   4.249 -12.655   3.970  1.00 60.95
>> N
>> ATOM804  CD2 HIS A 130   3.828 -14.777   4.284  1.00 59.58
>> C
>> ATOM805  CE1 HIS A 130   4.895 -13.022   5.066  1.00 60.24
>> C
>> ATOM806  NE2 HIS A 130   4.657 -14.305   5.279  1.00 60.16
>> N
>> ATOM807  N   ASP A 131   0.207 -14.462   3.285  1.00 54.76
>> N
>> ATOM808  CA  ASP A 131  -0.954 -15.320   3.512  1.00 54.01
>> C
>> ATOM809  C   ASP A 131  -1.040 -15.548   4.997  1.00 51.90
>> C
>> ATOM 80  OE1 GLN A  33   7.692  11.421  46.868  1.00 70.33
>> O
>>
>> Kindly suggest any way to correct the .pdb file so that it can be converted
>> to .gro file
>>
>> With Thanx,
>> Vivek
>>
>> 2008/8/12 Tsjerk Wassenaar <[EMAIL PROTECTED]>
>>>
>>> Well,
>>>
>>> sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
>>> file.pdb | sort | cut -b 2- > sorted.pdb
>>>
>>> sort of seems to do the trick. But it will place the chainless things
>>> first.
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>>> >
>>> >
>>> > vivek sharma wrote:
>>> >>
>>> >> Hi david,
>>> >> Thanx again, but I want to ask what changes need to be done there in
>>> >> such
>>> >> cases.
>>> >>
>>> >
>>> > The chain identifier needs to be continuous.  That is, if you have atoms
>>> > with chain identifiers like:
>>> >
>>> > A
>>> > A
>>> > B
>>> > A
>>> > C
>>> > A
>>> > A
>>> >
>>> > they should be re-written as:
>>> >
>>> > A
>>> > A
>>> > A
>>> > A
>>> > A
>>> > B
>>> > C
>>> >
>>> > This can be accomplished with some work in a simple text editor.
>>> >
>>> > -Justin
>>> >
>>> >> With Thanx,
>>> >> Vivek
>>> >>
>>> >> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]
>>> >> 

Re: [gmx-users] colour of the molecules

[Florian Haberl]

Hi,

On Wednesday, 13. August 2008,  huan wrote:
> Dear all gmx-users and developers,
>
> There are 6 different type of molecules in my simulation system. So how can
> I differentiate o recognize the type of those molecules? which files
> (topology, trr or others) should I look at?
>
> Any suggestions are appreciated.
> Thanks

please describe your problem with more details, have you setup a simulation?


>
>
>
>
> ___
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greetings,

Florian

-- 
---
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 Universitaet Erlangen/ Nuernberg
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 Telephone: +49(0) − 9131 − 85 26573
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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[gmx-users] Re: Force Field Parameters Nitrogen and Oxygen

[Vitaly Chaban]

> Date: Tue, 12 Aug 2008 16:36:16 -0500
> From: "Andy Shelley" <[EMAIL PROTECTED]>
> Subject: [gmx-users] Force Field Parameters Nitrogen and Oxygen
> To: gmx-users@gromacs.org
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><[EMAIL PROTECTED]>
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> I am trying to simulate air and have not been able to find force field
> parameters for a Nitrogen Nitrogen bond or Oxygen Oxygen bond.  If you could
> please direct me to where these could be found I would appreciate it.
>
> Thanks,
> Andy

There is a multitude of ways to deal with your system. It's very pity
you don't say us what you want to simulate exactly.

I think even if you use rigid O-O and N-N molecules it will not affect
the results of your simulation in most cases. Of course, it depends on
which properties you want to calculate exactly.

If you are about to simulate not air (telling the truth, it's not an
up-to-date task) but something  in the air atmosphere, you may want to
use a 1-atom model for each gas component. Although I'm sure proper N2
and O2 models can be easily found in literature.

The force bond constants are in fact similar enough to one another and
you may point out a constant for an atom pair resembling yours.
However, I cannot suggest you this way as absolutely correct one.

-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
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