Re: [AMBER] How to prepare the two tolopogy files when doing TI calculation?

From: <>
Date: Tue, 13 Apr 2010 08:35:46 -0400 (EDT)


there are many ways to do this and you should experiment a little to pick
the one that suits you best. One option is to build your system in leap
with both the initial and final states of the residue that changes (so two
copies of it, at the same place), then delete each one of them to write
your v0 and v1 prmtops.

An alternative would be to make two pdbs which only differ in the group
that changes and load them separately into leap. This leads to minor
coordinate deviation because of center of mass imaging, but sander will
correct for that.

The only important thing is that the v0 and v1 prmtops have the atoms that
do not change in the exact same order and (almost) same positions.

Kind Regards,


On Tue, April 13, 2010 8:29 am, fancy2012 wrote:
> Dear amber users,
> I want to do some TI calculation using GMX, and I have learned how to run
> it from the web tutorial. But there is still a problem. I don't know how
> to prepare the two topology files, which are initial and final states,
> respectively. For example, molecule A to molecule B, while the two
> molecules have only one different functional groups.
> Could somebody give me some suggestion on it? Any response will be highly
> appreciated! Thanks!
> All the best,
> fancy
> _______________________________________________
> AMBER mailing list

Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Tue Apr 13 2010 - 06:00:02 PDT
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