Also, have a read at acpype.googlecode.com. Alan
On 21 September 2010 06:36, manoj singh <mks.am...@gmail.com> wrote: > 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 > > http://ambermd.org/#AmberTools > > http://ambermd.org/antechamber/efz.html > > ffamber.cnsm.csulb.edu/*amb2gmx*.*pl* > > > On Tue, Sep 21, 2010 at 12:51 AM, vivek sharma <viveksharma.i...@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@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-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
