[gmx-users] On posre.itp
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.
> Up to you. Do you want to sample under unphysical restraints or not?
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