Please, take a look at acpypi.googlecode.com. I hope it can help you. Alan
On Wed, May 13, 2009 at 06:12, <[email protected]> wrote: > Subject: [gmx-users] DNA-ligand interactions with AMBER > > Dear Gromacs users > > I am simulating the interactions between ligands and DNA > using GROMACS with the AMBER force field, as implemented with > the AMBER PORT for GROMACS. Simulating DNA is actually > very easy with this protocol, but for the ligand some > problems arise. Until now we are constructing the > topology manually, but this became complicated for large > ligands. What is the best way to construct ligand > topologies with AMBER parameters, for using with GROMACS, > provided that we DO NOT have the AMBER package? > > Thank you very much in advance. > > Paulo Netz -- 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<< _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
