[gmx-users] MD on docked complex using AMBER FF

manoj singh mks.amber at gmail.com
Tue Sep 21 07:36:01 CEST 2010

First, you have to develop parameter for your molecule withing Amber. Then
you have to create .prmtop and .inpcrd files for your molecule, and than you
can convert the Amber topology to Gromacs topology. You will need AmberTools
and a script called amb2gmx.pl.

Following links would be helpful for you




On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma
<viveksharma.iitb at gmail.com>wrote:

> Hi There,
> I am trying to run molecular dynamics on a drug-enzyme complex using
> amber force field. I have done it earlier using gromos FF using
> drug-enzyme tutorial, I dont know if the parameter set (.mdp file)
> will be same or different while using AMBER FF.
> Any insight/comments into the matter may be of help if somebody has
> tried using AMBER FF for docked complex in GROMACS.
> Thanks in advance.
> regards,
> Vivek
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100921/1364d470/attachment.html>

More information about the gromacs.org_gmx-users mailing list