[gmx-users] On posre.itp

Mark Abraham Mark.Abraham at anu.edu.au
Sat May 7 11:32:58 CEST 2011

On 7/05/2011 7:16 PM, Mr Bernard Ramos wrote:
> Thanks for the response. I will be doing a simple MD 
> without the positional restraints. How do I go about reviewing the 
> code for posres? What I did was to add new ff parameters for a new 
> residue I introduced. May I please know what file in the 
> program determines the posres so that I can revew them. Thanks.

Please give full descriptions the first time. I posted a noob question 
on the AMBER mailing list a few months back, and would never have gotten 
the problem solved except that I included some details that I thought 
were irrelevant, and someone spotted my problem. We've all got better 
things to do than play question-and-answer. You might have invented some 
atom names that pdb2gmx doesn't know how to cope with - but you haven't 
said whether your apparently erronously generated position restraints 
are specific to your new residue or not. Unfortunately you haven't 
shared your atom names after I suggested the atom names were probably 
the problem, and I'm not going to make guesses. There's various 
databases in $GMXLIB/share/top for various force fields, but I don't 
know your GROMACS version either...

I don't think looking at the code will lead to a solution.


> --- On *Sat, 5/7/11, Mark Abraham /<Mark.Abraham at anu.edu.au>/* wrote:
>     From: Mark Abraham <Mark.Abraham at anu.edu.au>
>     Subject: Re: [gmx-users] On posre.itp
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Saturday, May 7, 2011, 5:10 PM
>     On 7/05/2011 7:01 PM, Mr Bernard Ramos wrote:
>>     Hi everyone!
>>     I was able to generate a pdb file in which the hydrogens for the
>>     molecule are already included (that way I avoided using the hdb
>>     file for the pdb2gmx). However, when I checked the posre.itp, the
>>     some of the restraints were applied to the hydrogens. Is this
>>     correct because I am not sure since I what I know is that the
>>     restraints should be applied to heavy atoms.
>     Maybe your atom names are confusing pdb2gmx. Maybe you're
>     comparing apples and oranges with the indices in the coordinate
>     file and the indices in the posres.itp (which are relative to the
>     [atoms], IIRC).
>>     Are the positional restraints needed only for the equalibration
>>     step but not for the production runs in normal MD simulations.
>>     Thanks.
>     Up to you. Do you want to sample under unphysical restraints or not?
>     Mark
>     -----Inline Attachment Follows-----
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