vivek sharma wrote:
Hi Andreas,
Thanks for your response.
But I am not finding option for AMBER forcefield in gromacs (during
pdb2gmx step). which of the 9 force-field I should use for the same.
You have to download and install the ffamber ports:
http://chemistry.csulb.edu/ffamber/
-Justin
With Thanks,
Vivek
2008/11/7 Kukol, Andreas <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
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: [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
[mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>] 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
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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