[gmx-users] Re: Ligand & Receptor

[Jack Shultz]

This is neat! Thanks
http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs

On Fri, Jun 26, 2009 at 9:36 AM, Alan<alanwilter at gmail.com> wrote:
> Hi there,
> How about taking a look at acpypi.googlecode.com and its wikis?
> I hope it can help you.
> Alan
> 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.
>>>http://www.bio.cam.ac.uk/~awd28<<
>
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org