*If you are familiar to ambertools (tleap mainly), so you can create your molecule there, save the amber parameters and use acpype to convert from amber to gromacs format.
*Thanks Alan, I use tleap and then amb2gmx.pl. It works great, the only problem is the NAc groups aren't restrained properly so have to manually edit them in. I'll have to do some reading about acpype... On 20 May 2010 13:28, Alan <alanwil...@gmail.com> wrote: > Dear Oliver, > > > On Thu, May 20, 2010 at 13:21, <gmx-users-requ...@gromacs.org> wrote: > >> I'm using GLYCAM06, so it involves a bit more effort to generate a .top >> and >> .gro file than just using pdb2gmx but I thought I'd leave it out as I just >> wanted to explain the method I use to include it. Apologies for the >> confusion! >> > > If you are familiar to ambertools (tleap mainly), so you can create your > molecule there, save the amber parameters and use acpype to convert from > amber to gromacs format. > > Alan > > > -- > 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 <http://www.bio.cam.ac.uk/%7Eawd28><< > > -- > 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/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/mailing_lists/users.php >
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