[gmx-users] Re: Ligand & Receptor

Alan alanwilter at gmail.com
Fri Jun 26 15:36:14 CEST 2009

Hi there,
How about taking a look at acpypi.googlecode.com and its wikis?

I hope it can help you.


On Fri, Jun 26, 2009 at 14:27, <gmx-users-request at gromacs.org> wrote:

> Hello,
> I'm trying to figure out how I can merge the ligand and receptor
> files. I used this script to prep a ligand I treated with GAFF
> perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand
> This results in ligand.top & ligand.gro
> Then I prepped a receptor
> pdb2gmx_d -f fzd2.pdb -ff amber03 -o conf.pdb
> Is there some way to merge these structures and then simulate with gromacs?
> --
> Jack
> http://drugdiscoveryathome.com
> http://hydrogenathome.org

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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