Hi Andreas,<br> Thanks for your response.<br>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.<br><br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">
2008/11/7 Kukol, Andreas <span dir="ltr"><<a href="mailto:a.kukol@herts.ac.uk">a.kukol@herts.ac.uk</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
Autodock4 uses the AMBER forcefield, so that would be a good starting point for gromacs as well.<br>
<br>
In order to set the temperature for a particular group<br>
1) you generate an index file containing all the atoms in your GROUP<br>
2) in your mdp-file specify GROUP as a separate temperature coupling group and specify the temperature you want<br>
3) use grompp with -n yourindexfile.ndx<br>
<br>
Note sure, if this is makes physically sense though.<br>
<br>
Andreas<br>
<br>
<br>
>>>>>>>>>>>>>>>>><br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] On Behalf Of vivek sharma<br>
Sent: 07 November 2008 09:00<br>
To: Discussion list for GROMACS users<br>
Subject: [gmx-users] Running MDS over docked poses<br>
<div><div></div><div class="Wj3C7c"><br>
Hi There,<br>
I am trying to run MDS over some docked result generated by Autodock4, but I am not sure of the forcefield I should use.<br>
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.<br>
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 ?<br>
<br>
waiting for some suggestion.<br>
<br>
With Thanks,<br>
Vivek<br>
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