----- Original Message ----- From: "Justin A. Lemkul" <jalem...@vt.edu> Date: Thursday, July 1, 2010 9:58 Subject: Re: [gmx-users] Capping residues To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > > Sai Pooja wrote: > >Hi, > > > >1) What capping residues are recognized by charmm implemented > on gromacs in the latest git version? > > It looks like there aren't any. Check the .rtp file to be sure. There aren't. I had a discussion with Par Bjelkmar a while back about including some, but I don't recall the outcome. Mark > >I was trying to use ACE for acetyl but it is not recognized by > pdb2gmx.> > > > >2) Is it possible to define caps at residues other than those > at the termini? > > > > What exactly do you consider a cap? Usually a capping > residue is applied only to N- and C-termini. If you're > trying to make some sort of modified sidechain, then you have to > look into parameterizing it yourself. > > http://www.gromacs.org/Documentation/How-tos/Parameterization > > -Justin > > >Regards > >Pooja > > > >-- > >Quaerendo Invenietis-Seek and you shall discover. > > > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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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