[gmx-users] topology file for thermodynamic integration
tsurui at med.juntendo.ac.jp
Wed Oct 26 17:42:41 CEST 2005
Thank you for you kind mail.
Actually, I have read the manual, especially Chapter 5, a few times. However
the description about the topology file for TI is rather abstract for me,
and I could not be certain of it. I feel your mail showed me essential
points and gave explanation from another point.
Any way, I will try, as you suggested, a simple case.
----- Original Message -----
From: "Maik Goette" <mgoette at mpi-bpc.mpg.de>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, October 26, 2005 8:20 PM
Subject: Re: [gmx-users] topology file for thermodynamic integration
> I don't really know, if there is a tutorial.
> The way how to use FEP(TI) is written in the manual quite well.
> A "short" discription, of what you may want to do is:
> Add dummy atoms to your topology file, which resemble the atoms of the
> mutated AA.
> You can insert the full AA with dummies and use energy group exclusions
> or just insert the atoms as dummies, which are not able to be
> "converted" from other ones of the original AA.
> Then you have to insert the B-values (principles behind that are also in
> the manual), in fact Atomtype, Mass and charge of the B-State.
> It depends on the FF, what you have to do in the
> bonds,pairs,angles,dihedrals section.
> If I'm right, OPLS is able to "interpolate" the values by itself, in
> others (GMX) you have to manually include the B-values in the topology
> file for all atoms, that have a B-value in the atoms section.
> Don't forget that, maybe atoms itself don't change, but e.g. their
> partial charges . These also need B-values and for that case, their
> further parameters have to be changed, too...
> Perhaps you should try an ALA->GLY or some other easy perturbation.
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
> Hiromichi Tsurui wrote:
>> Hi, all of Gromacs users;
>> I would like to calculate binding free-energy of protein and peptide, or
>> difference of that between wild type and mutation-containing one. I am
>> going to use thermodynamic integration method. Could anyone let me know
>> a good tutorial ? I want to know especially how to describe topology
>> Thank you.
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