[gmx-users] ATP, GTP and REX

[Robert Fenwick]

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?

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