[gmx-users] Running MDS over docked poses

[Kukol, Andreas]

Hi,

Autodock4 uses the AMBER forcefield, so that would be a good starting point for gromacs as well.

In order to set the temperature for a particular group
1) you generate an index file containing all the atoms in your GROUP
2) in your mdp-file specify GROUP as a separate temperature coupling group and specify the temperature you want
3) use grompp with -n yourindexfile.ndx

Note sure, if this is makes physically sense though.

Andreas


>>>>>>>>>>>>>>>>>
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of vivek sharma
Sent: 07 November 2008 09:00
To: Discussion list for GROMACS users
Subject: [gmx-users] Running MDS over docked poses

 Hi There,
I am trying to run MDS over some docked result generated by Autodock4, but I am not sure of the forcefield I should use.
If anybody have tried doing it before, please guide me for the same. For generating topology of ligand, I am using PRODRG server, which has limited option for forcefield.
Also, how can I give the parameters for varying temperature of a particular group during the MDS, like how canI define the steps I want to vary it ?

waiting for some suggestion.

With Thanks,
Vivek