Re: [gmx-users] OPLS-AA Unknown Atomtype

[Yao Yao]

Hi Justin,

Thanks for your last reply. Now it seems that OPLS has known the atomtypes 
after I added those CA1, ... to ffoplsaanb.itp,
but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it 
still gives errors like,

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
Generated 338253 of the 338253 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 338253 of the 338253 1-4 parameter combinations

ERROR 1 [file cro.top, line 37]:
  No default Bond types


ERROR 2 [file cro.top, line 71]:
  No default Angle types


ERROR 3 [file cro.top, line 72]:
  No default Angle types


ERROR 4 [file cro.top, line 85]:
  No default Angle types


ERROR 5 [file cro.top, line 91]:
  No default Ryckaert-Bell. types


ERROR 6 [file cro.top, line 92]:
  No default Ryckaert-Bell. types


ERROR 7 [file cro.top, line 93]:
  No default Ryckaert-Bell. types


ERROR 8 [file cro.top, line 108]:
  No default Ryckaert-Bell. types


ERROR 9 [file cro.top, line 112]:
  No default Proper Dih. types


ERROR 10 [file cro.top, line 113]:
  No default Proper Dih. types


ERROR 11 [file cro.top, line 114]:
  No default Proper Dih. types

Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file cro.top, line 142]:
  System has non-zero total charge: -1.022478e+00
  


processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

---
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 11 errors in input file(s)
---

I do double-check those bondtypes, angles, and interactions mentioned in the 
errors, and I am pretty sure I have already declared those values in the 
ffoplsaabon.itp. 
Is there any other file I also need to mention those values?

Thanks,

Yao














From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Tuesday, August 23, 2011 2:07 PM
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype



Yao Yao wrote:
> Hi Justin,
> 
> Thanks for your reply. Here is the exact error message,
> 
> 
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> processing topology...
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> 
> ---
> Program grompp, VERSION 4.0.7
> Source code file: toppush.c, line: 620
> 
> Fatal error:
> Unknown bond_atomtype CA1
> 
> ---
> ~~
> 
> I understand that I have not inserted CA1 into "atomtypes.atp". because if I 
> add CA1 as a new atom, I have to mention all bonds, angles, dihedrals of it.

The atomtypes.atp file is irrelevant here; it is only used by pdb2gmx.  What 
you are trying to avoid is what you have to do - if you introduce a new atom 
type and intend to use it in any bonded interactions, you must introduce 
relevant parameters for all the interactions in which it will participate.

> So I denoted the type of it as a known carbon atom in my topology file (in 
> the attachment). I thought in OPLS-AA, CA1 can "cite" this known atom since 
> CA1 is just a name.

Names and types are different.  You can name an atom anything you like, but 
atom types must be judiciously assigned.

> Meanwhile, in the ffbonded.itp and ffnonbonded.itp, I still use CA1 to give 
> bonds, angles, and dihedrals of CA1.
> 

If you have inserted all of the correct parameters in these files, you would 
not receive the error above.  Perhaps herein lies the problem - if you have 
modified ffnonbonded.itp (which belongs to the force field organization of the 
4.5.x series), it will have no effect on a 4.0.7 executable, which is being 
called above.  So (at least) one of two possibilities is true:

1. You're not using the Gromacs version you intend to.
2. You haven't introduced all of the parameters you need to.

The bond_atomtype values are assigned in ffnonbonded.itp (counterintuitive, I 
know, but that's how it 

[gmx-users] Phd positions available

[Giovanni Bussi]

Dear all,

since many people in our group are gromacs users, this announcement
could make some sense on the gmx mailing list. Please forward it to
interested people.

Best wishes,

Giovanni Bussi



***PhD positions at SISSA in Physics and Chemistry of Biological Systems

There are 3 positions available for the PhD in Physics and Chemistry
of Biological Systems at the International School for Advanced
Studies, Trieste, Italy.

Applicants should have a good background in Physics, Chemistry or
related subjects and are expected to obtain their Laurea Specialistica
or equivalent degree by Autumn 2011.

Applicants will be first screened based on their CV (educational track
record, letters of presentation, preprints or publications). Those
that pass the preliminary screening will be invited to participate to
the local selection taking place on October 5 and 6.

Admitted students will have the opportunity to follow a one-year
educational program in an international and interdisciplinary
environment, followed by two or three years of active research in one
of the following areas:

* structural bioinformatics,
* statistical mechanics of complex molecular systems,
* biomolecular simulations,
* simulations of rare events.

For further information about the available research lines, and past
entrance exams see the Statistical and Biological Physics Sector
website.

To apply:
The application should be filled exclusively online at the following
address: www.sissa.it/applications/phd . The application deadline is
September 19th.
The complete official announcement can be download here.
Notice that SISSA can cover, in full or in part, the expenses of
students who are admitted to the local entrance exam. Please contact
p...@sissa.it for further information.

About SISSA:
The International School for Advanced Studies of Trieste. SISSA was
the first Italian university to offer the PhD degree, and has
continued to do so with notable success. Since its founding in 1978,
SISSA has prepared more than 500 young people for careers in research
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According to a recent independent comprehensive academic survey SISSA
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receive a contribution during their maternity leave. Students are
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***Start Date November 2011

***Duration 3 to 4 years

***Funding Source Italian Ministry of University

***Salary on grant Ministerial PhD fellowship integrated by SISSA for
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contributions towards house rent and purchase of personal laptop.

***Contact person Cristian Micheletti

***email miche...@sissa.it

***Group web page: www.sissa.it/sbp
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Re: [gmx-users] OPLS-AA Unknown Atomtype

[Justin A. Lemkul]

Yao Yao wrote:

Hi Justin,

Thanks for your last reply. Now it seems that OPLS has known the 
atomtypes after I added those CA1, ... to ffoplsaanb.itp,
but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, 
it still gives errors like,


Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp

Generated 338253 of the 338253 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 338253 of the 338253 1-4 parameter combinations

ERROR 1 [file cro.top, line 37]:
  No default Bond types


ERROR 2 [file cro.top, line 71]:
  No default Angle types


ERROR 3 [file cro.top, line 72]:
  No default Angle types


ERROR 4 [file cro.top, line 85]:
  No default Angle types


ERROR 5 [file cro.top, line 91]:
  No default Ryckaert-Bell. types


ERROR 6 [file cro.top, line 92]:
  No default Ryckaert-Bell. types


ERROR 7 [file cro.top, line 93]:
  No default Ryckaert-Bell. types


ERROR 8 [file cro.top, line 108]:
  No default Ryckaert-Bell. types


ERROR 9 [file cro.top, line 112]:
  No default Proper Dih. types


ERROR 10 [file cro.top, line 113]:
  No default Proper Dih. types


ERROR 11 [file cro.top, line 114]:
  No default Proper Dih. types

Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file cro.top, line 142]:
  System has non-zero total charge: -1.022478e+00
 



This total charge suggests that your topology is badly broken.



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...

There was 1 note

---
Program grompp, VERSION 4.0.7
Source code file: grompp.c, line: 986

Fatal error:
There were 11 errors in input file(s)
---

I do double-check those bondtypes, angles, and interactions mentioned in 
the errors, and I am pretty sure I have already declared those values in 
the ffoplsaabon.itp. 
Is there any other file I also need to mention those values?




If these types were actually present in ffoplsaabon.itp, then you wouldn't get 
these errors.  Double check again.


-Justin

--


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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[gmx-users] Error found on grompp - energy minimization

[ITHAYARAJA]

Dear sir,
I struck with the following error when i perform energy minimization. I
unable to understand what did it mean? please make me clear.

So kindly do the needful.

Fatal error:
Atomtype CR1 not found

-- 
**
Ithayaraja M,
Research Scholar,
Department of Bionformatics,
Bharathiar University,
Coimbatore 641 046,
Tamil Nadu
India
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Re: [gmx-users] Error found on grompp - energy minimization

[Mark Abraham]

On 29/08/2011 9:18 PM, ITHAYARAJA wrote:

Dear sir,
I struck with the following error when i perform energy minimization. 
I unable to understand what did it mean? please make me clear.


So kindly do the needful.

Fatal error:
Atomtype CR1 not found


One of your molecules is trying to use an atomtype that isn't defined in 
your force field. However we can't guess why without a lot more 
information. See http://www.gromacs.org/Support


Mark
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[gmx-users] Re: gromacs question topologie

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list, 
particularly if the discussion was previously carried out there.  I am not a 
private tutor.


Joschua Sterzenbach wrote:

Hi

is in the coordinate file only the geometry of the molecule?



Yes.  Have a look at its contents - all you'll find in most common formats are 
the (x,y,z) coordinates of the named atoms.



I ask because I only have the geometry.

Do I get the topologie out of the geometry or from where comes it?



Please do some basic tutorial material to understand the Gromacs workflow.  For 
residue-based biomolecules like proteins and nucleic acids, use pdb2gmx.  For 
other molecules, g_x2top can create basic topologies for a limited number of 
force fields and molecules.  Otherwise, you'll have to obtain the topology by 
some other means.  There are other programs on the User Contributions page of 
the Gromacs site that can produce topologies for arbitrary molecules.


You haven't said yet what you're working with, so all I can do is venture 
guesses.

-Justin

The questions corresponds to this: 
http://www.mail-archive.com/gmx-users@gromacs.org/msg43478.html


Thanks
Regards


--


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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[gmx-users] Re: Difficulty building a topology for a synthetic, branched PEG-peptide molecule [SOLVED]

[Pablo Englebienne]

That's a long bond. Does your reference length in specbond.dat suit it?
IIRC there should be some evidence in the output of the special bond
being formed if it actually is. If not, your symptoms are probably related
Hi Mark, indeed, I think that was part of the problem. pdb2gmx indeed 
outputs a message when a specbond.dat rule is matched and a bond formed.


In case it helps to someone else or for reference purposes, I finally 
managed to solve the issue.


Some of the lessons I learned:
- make sure that the residues/atoms in specbond.dat were correct (I had 
defined a number of residues for termini and mid-chain PEG and 
connectors, and I got them confused at some point, so not all of them 
were being recognized properly). The "dangling bond at at least one of 
the terminal ends" given by pdb2gmx is most likely due to this and/or 
the protonation state of the residues connecting the fragments
- each fragment is assigned a different chain letter in the source PDB 
file; in my case, for a system like


[N-(peptide1)-C]-[N-(PEG)-C]-[N-(peptide2)-Lys-C]
|
NZ
|
[C-(PEG)-N]-[C-(peptide3)-N]

each fragment in square brackets is assigned a different chain name in 
[A-E] in the PDB file:


ATOM123  N   ARG A   1  74.024  13.299  50.237  1.00  
0.00   N1+

 ^
- always list the atoms within a chain in an N-to-C direction. This 
means that the main branch is defined first, and then the branching 
point is defined in an N-to-C direction, even if it is counterintuitive 
by the way they are connected. specbond.dat takes good care of setting 
up the connection in all cases (as long as they are well defined...).

- the PEG residues need to be defined as type "Other" in residues.dat
- call pdb2gmx to manually assign the termini and Lys protonation states 
manually, and to merge the chains into a single molecule:


pdb2gmx-ter  -f  substrate.pdb-chainsep  interactive-lys

-> the "internal" termini (i.e., the ones that are peptide termini but 
are connected to a PEG chain) need to be given a protonation state of 
"None", while the "real" termini can be assigned as charged or neutral, 
depending on the conditions



Oh, and well done for constructing a good question. You would likely not have 
gotten anywhere giving less detail :)
Thanks, it actually helped putting everything in writing, as it pointed 
out the few things that I hadn't yet looked at in detail...


Pablo Englebienne, PhD
Dept. of Biomedical Engineering
Dept. of Chemistry and Chemical Engineering
Institute for Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

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[gmx-users] simulation at higher temperatures

[arun kumar]

Hi friends,

As a part of my work i have to do simulation at higher temperature (400K or
more) to study the folding, unfolding and stability of protein, for that i
kept simulation for 3ns at 400k (400k temperature both in equilibration and
production) keeping all the other parameters as usual (time step 2fs,
explicit solvent model SPC, equilibration with NVT and NPT ensembles for
100ps each  ). the simulation was completed but ,
1. in trajectory i found that protein is comming out of the box (cubic box
-d 1.0) i think may be the box size was not sufficient  (and i know that
when we increase the temperature the velocity of atoms will increase).
2.  when i save the structure with minimum energy  and saw in pymol i found
the side chains, hydrogens was broken through out the protein.
3. later i used the command ( trajconv -s md.tpr -f md.trr -o protein.pdb
-pbc nojump -dt 10 ) to save the conformations at each 10 ps and to see the
conformational changes by playing it as a movie in pymol , but i found a
single conformation was just shaking through out the movie (this is
happening in normal simulation also)

later i read in gmx user problems that most of the force field parameters
are calculated at room temperature, so in that case what are the parameters
and forcefield that we need to fallow for higher temperature simulations.

so can any one please takes time to explain this, it would be helpful for me
to study further.

Thanking you.

with regards
-- 
Arun Kumar Somavarapu
Center for Bioinformatics
Pondicherry University
Kalapet
Puducherry-605014
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Re: [gmx-users] simulation at higher temperatures

[Justin A. Lemkul]

arun kumar wrote:


Hi friends,
 
As a part of my work i have to do simulation at higher temperature (400K 
or more) to study the folding, unfolding and stability of protein, for 
that i kept simulation for 3ns at 400k (400k temperature both in 
equilibration and production) keeping all the other parameters as usual 
(time step 2fs, explicit solvent model SPC, equilibration with NVT and 
NPT ensembles for 100ps each  ). the simulation was completed but ,


I doubt any simulation, even of the simplest protein, is "complete" at 3 ns.

1. in trajectory i found that protein is comming out of the box (cubic 
box -d 1.0) i think may be the box size was not sufficient  (and i know 
that when we increase the temperature the velocity of atoms will increase).


Please see FAQ #3 under the following section:

http://www.gromacs.org/Documentation/FAQs#Analysis_and_Visualization

2.  when i save the structure with minimum energy  and saw in pymol i 
found the side chains, hydrogens was broken through out the protein.


Same as above.

3. later i used the command ( trajconv -s md.tpr -f md.trr -o 
protein.pdb -pbc nojump -dt 10 ) to save the conformations at each 10 ps 
and to see the conformational changes by playing it as a movie in pymol 
, but i found a single conformation was just shaking through out the 
movie (this is happening in normal simulation also)  


Your simulation length is inadequate to view any conformational changes.  These 
types of motions can require hundreds of ns, if not more (depending on the size 
of the protein), to visualize.


-Justin



later i read in gmx user problems that most of the force field 
parameters are calculated at room temperature, so in that case what are 
the parameters and forcefield that we need to fallow for higher 
temperature simulations.


so can any one please takes time to explain this, it would be helpful 
for me to study further.


Thanking you.

with regards  
--

Arun Kumar Somavarapu
Center for Bioinformatics
Pondicherry University
Kalapet
Puducherry-605014



--


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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[gmx-users] g_lie

[pawan raghav]

g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either p or w and -Cqq for either p  or w. My question is when
using only p for -Elj and Vl-s el>p for  -Cqq, how the LJ and EL
terms calculated for ligand-water interaction or in vice-versa condition for
ligand-protein interactions to complete the deltaG equation?

-- 
Pawan
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Re: [gmx-users] OPLS-AA Unknown Atomtype

[Yao Yao]

HI Justin,

I met these errors when I grompp to do 1st-time energy minimization before I 
planned to add the ions.

So I do not think ions addition will help. And I double-checked the angles, 
bonds,  mentioned in the ffoplsaabon.itp, they are there.
So I do not know any other files I may need to modify.

Thanks,

yao





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Monday, August 29, 2011 3:41 AM
Subject: Re: [gmx-users] OPLS-AA Unknown Atomtype



Yao Yao wrote:
> Hi Justin,
> 
> Thanks for your last reply. Now it seems that OPLS has known the atomtypes 
> after I added those CA1, ... to ffoplsaanb.itp,
> but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it 
> still gives errors like,
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> processing topology...
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp
> Generated 338253 of the 338253 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 338253 of the 338253 1-4 parameter combinations
> 
> ERROR 1 [file cro.top, line 37]:
>   No default Bond types
> 
> 
> ERROR 2 [file cro.top, line 71]:
>   No default Angle types
> 
> 
> ERROR 3 [file cro.top, line 72]:
>   No default Angle types
> 
> 
> ERROR 4 [file cro.top, line 85]:
>   No default Angle types
> 
> 
> ERROR 5 [file cro.top, line 91]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 6 [file cro.top, line 92]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 7 [file cro.top, line 93]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 8 [file cro.top, line 108]:
>   No default Ryckaert-Bell. types
> 
> 
> ERROR 9 [file cro.top, line 112]:
>   No default Proper Dih. types
> 
> 
> ERROR 10 [file cro.top, line 113]:
>   No default Proper Dih. types
> 
> 
> ERROR 11 [file cro.top, line 114]:
>   No default Proper Dih. types
> 
> Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
> Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 2 bonded neighbours molecule type 'SOL'
> 
> NOTE 1 [file cro.top, line 142]:
>   System has non-zero total charge: -1.022478e+00
>  

This total charge suggests that your topology is badly broken.

> 
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> 
> There was 1 note
> 
> ---
> Program grompp, VERSION 4.0.7
> Source code file: grompp.c, line: 986
> 
> Fatal error:
> There were 11 errors in input file(s)
> ---
> 
> I do double-check those bondtypes, angles, and interactions mentioned in the 
> errors, and I am pretty sure I have already declared those values in the 
> ffoplsaabon.itp. Is there any other file I also need to mention those values?
> 

If these types were actually present in ffoplsaabon.itp, then you wouldn't get 
these errors.  Double check again.

-Justin

-- 

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] OPLS-AA Unknown Atomtype

[Justin A. Lemkul]

Yao Yao wrote:

HI Justin,

I met these errors when I grompp to do 1st-time energy minimization 
before I planned to add the ions.

So I do not think ions addition will help. And I double-checked the


The net charge problem cannot be solved by adding ions.  A fractional charge of 
that magnitude indicates the charges in the topology are wrong.



angles, bonds,  mentioned in the ffoplsaabon.itp, they are there.
So I do not know any other files I may need to modify.



The only file that contains [bondtypes], [angletypes], etc is ffoplsaabon.itp, 
so if the entries are indeed there, have the correct format, and are placed 
appropriately, you wouldn't be getting this error.  So unless you post the exact 
lines in their exact context, I'm left to assume that you've done something else 
wrong.


-Justin


Thanks,

yao



*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Monday, August 29, 2011 3:41 AM
*Subject:* Re: [gmx-users] OPLS-AA Unknown Atomtype



Yao Yao wrote:
 > Hi Justin,
 >
 > Thanks for your last reply. Now it seems that OPLS has known the 
atomtypes after I added those CA1, ... to ffoplsaanb.itp,
 > but after I claim all the angles, dihedrals, ... in the 
ffoplsaabon.itp, it still gives errors like,

 >
 > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
 > checking input for internal consistency...
 > processing topology...
 > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffoplsaa.itp
 > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffoplsaanb.itp
 > Opening library file 
/share/apps/gromacs407/share/gromacs/top/ffoplsaabon.itp

 > Generated 338253 of the 338253 non-bonded parameter combinations
 > Generating 1-4 interactions: fudge = 0.5
 > Generated 338253 of the 338253 1-4 parameter combinations
 >
 > ERROR 1 [file cro.top, line 37]:
 >  No default Bond types
 >
 >
 > ERROR 2 [file cro.top, line 71]:
 >  No default Angle types
 >
 >
 > ERROR 3 [file cro.top, line 72]:
 >  No default Angle types
 >
 >
 > ERROR 4 [file cro.top, line 85]:
 >  No default Angle types
 >
 >
 > ERROR 5 [file cro.top, line 91]:
 >  No default Ryckaert-Bell. types
 >
 >
 > ERROR 6 [file cro.top, line 92]:
 >  No default Ryckaert-Bell. types
 >
 >
 > ERROR 7 [file cro.top, line 93]:
 >  No default Ryckaert-Bell. types
 >
 >
 > ERROR 8 [file cro.top, line 108]:
 >  No default Ryckaert-Bell. types
 >
 >
 > ERROR 9 [file cro.top, line 112]:
 >  No default Proper Dih. types
 >
 >
 > ERROR 10 [file cro.top, line 113]:
 >  No default Proper Dih. types
 >
 >
 > ERROR 11 [file cro.top, line 114]:
 >  No default Proper Dih. types
 >
 > Opening library file /share/apps/gromacs407/share/gromacs/top/spc.itp
 > Opening library file /share/apps/gromacs407/share/gromacs/top/ions.itp
 > Excluding 3 bonded neighbours molecule type 'Protein'
 > Excluding 2 bonded neighbours molecule type 'SOL'
 > Excluding 2 bonded neighbours molecule type 'SOL'
 >
 > NOTE 1 [file cro.top, line 142]:
 >  System has non-zero total charge: -1.022478e+00
 > 


This total charge suggests that your topology is badly broken.

 >
 > processing coordinates...
 > double-checking input for internal consistency...
 > renumbering atomtypes...
 > converting bonded parameters...
 >
 > There was 1 note
 >
 > ---
 > Program grompp, VERSION 4.0.7
 > Source code file: grompp.c, line: 986
 >
 > Fatal error:
 > There were 11 errors in input file(s)
 > ---
 >
 > I do double-check those bondtypes, angles, and interactions mentioned 
in the errors, and I am pretty sure I have already declared those values 
in the ffoplsaabon.itp. Is there any other file I also need to mention 
those values?

 >

If these types were actually present in ffoplsaabon.itp, then you 
wouldn't get these errors.  Double check again.


-Justin

-- 

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/

[gmx-users] MARTINI / all-atom mapping

[Michael Daily]

Hi all,

I am trying to reverse-map some martini lipids to united atom.  In order to
do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping.  I
cannot find this, only an imprecise graphic, in the MARTINI paper; the
martini.itp file doesn't appear to list which heavy atoms are represented by
each CG bead either.  For example, I'm looking for something like:

'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'],
'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'],
'GL1' : ['C13', 'O14', 'C15', 'O16'],
'GL2' : ['C32', 'O33', 'C34', 'O35'],

etc.

For some atoms it's obvious which MARTINI groups they belong in, but others
on the borderline are not obvious.  For example, does C12 belong in PO4 or
GL1?

Anybody have a master list like this?

Thanks,
Mike

-- 

Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)
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[gmx-users] restarting a crashed job

[Payman Pirzadeh]

Hello,

My simulation crashed in the middle and I used the "-cpi checkpoint.cpt
-append" option to continue. However, GROMACS cannot continue and complains
about not being able to open the corresponding .trr file. I checked my
folder, the trr file is there and the name is the same as the *.tpr and
*.cpt files. What else could have caused this problem?

 

Thanks.

 

P.

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Re: [gmx-users] restarting a crashed job

[Mark Abraham]

On 30/08/2011 1:14 PM, Payman Pirzadeh wrote:


Hello,

My simulation crashed in the middle and I used the "/--cpi 
checkpoint.cpt  --append"/ option to continue. However, GROMACS cannot 
continue and complains about not being able to open the corresponding 
.trr file. I checked my folder, the trr file is there and the name is 
the same as the *.tpr and *.cpt files. What else could have caused 
this problem?




Some kind of filesystem-based locking mechanism sounds most likely. If a 
zombie process of the old run still has the file, you might not be able 
to open it again. Also, check the file permissions.


Mark
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