I think I've got the answer. It is on the input pdb file. The heavy atoms need
to be labeled properly. thanks
--- On Sat, 5/7/11, Mr Bernard Ramos <bgrquan...@yahoo.com> wrote:
From: Mr Bernard Ramos <bgrquan...@yahoo.com>
Subject: Re: [gmx-users] On posre.itp
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Saturday, May 7, 2011, 5:16 PM
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.
--- On Sat, 5/7/11, Mark Abraham <mark.abra...@anu.edu.au> wrote:
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] On posre.itp
To: "Discussion list for GROMACS users" <gmx-users@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
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