On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi <n.gandh...@gmail.com> wrote:
> Dear Users, > > I have a system consisting of peptides and a linear carbohydrate. > Initially I tried to simulate these peptides using virtual sites and > it worked. I can use pdb2gmx for building virtual sites on protein > whereas I have an itp file for the carbohydrate. Yes you can modify the top file by hand to use itp files generated in two different ways. > Is it possible to > apply virtual site to a carbohydrate along with the peptides? > If you have an rtp file for you carbohydrate you should be able to run pdb2gmx and then you should also be able to generate vsite. Or you can generate them using your own scripts. Of course you only need them if you have the respective groups (e.g. CH3). Roland > > -- > Regards, > Dr. Neha S. Gandhi, > Curtin Research Fellow, > School of Biomedical Sciences, > Curtin University, > Perth GPO U1987 > Australia > LinkedIn > Research Gate > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
