[gmx-users] ATP, GTP and REX

[Justin A. Lemkul]

Quoting Robert Fenwick <rbf22 at mole.bio.cam.ac.uk>:

>
>
> Hi,
>
> I would like to make some unrestrained simulations of ATP and GTP
> binding proteins and wondered if there were any topology files
> floating about for OPLSAA or the GROMOS96.1 forcefields for these two
> ligands?

ATP is present in ffG43a1 (have a look at the .rtp file), and GTP has been
discussed across this list within the last few days (check out the archives).

-Justin

>
> I understand that the gmx forcefields have been deprecated and that I
> should use one of the newer ones, however there are not that many
> ligand topology files about.
>
> I am just starting out, so any suggestions would be welcome. The
> systems are approximately 300 residues in size and I am interested in
> the stability and rms fluctuations of the systems.
>
> A secondary question is that of the AMBER forcefields, I am using the
> 3.3.2 version, however the amber files state specifically to use the
> port for the relevant version, one of which is missing for 3.3.2. Is
> it safe to use the 3.3.1 amber ff port with version 3.3.2 of GROMACS?
>
> Finally, if anyone can point me in the direction of a small test
> project that does some simple replica exchange, with some
> instructions as to how to get it to run, I would be very grateful.
>
>
> Bryn
>
>
>
>
>
>
>
>
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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