[gmx-users] co-solvent simulation
yao0o at ymail.com
Sun Feb 12 07:47:24 CET 2012
Thanks for your reply. I have not figured out what the problem. BUt I am thinking if I have two proteins in my system,
like simulating the protein-protein interaction, what I should call the second protein for [moleculetype] in my .top, still "protein"?
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, February 11, 2012 9:39 PM
Subject: Re: [gmx-users] co-solvent simulation
On 12/02/2012 4:16 PM, Yao Yao wrote:
I am simulating a protein in glycerol solution in amber03 ff and followed "http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents".
>Since glycerol is not available in amber03.ff by default, I built it in the ffbonded.itp
You should not need to touch this file to model glycerol. There are
no atom or interaction types that are materially different from
those on peptide side chains.
>For test purpose, I then made a itp for it and solvate it as a protein and changed .top file accordingly, everything seems fine when I grompp,
>but when I insert it as a co-solvent, it shows like that I never did claim any bond angles, dihedrals, .... even when I #include its .itp and change #mols in my new topology.
You need to work out what is different in the two cases. The diff
tool can be useful here. There is no fundamental difference in the
.top construction for the two cases you are considering - only in
construction of the initial coordinates.
>I guess the problem is if I do not claim the co-solvent as a protein, ff will not go to ffbonded.itp to recognize the new interactions.
>Is there any other file for co-solvent interactions I need to change?
The ffbonded.itp file is #included regardless of what you name your
moleculetypes. You may not be #including the correct one - but then
again I think you should only have the standard one in the first
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