[gmx-users] Capping residues
mark.abraham at anu.edu.au
Thu Jul 1 02:39:59 CEST 2010
----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Thursday, July 1, 2010 9:58
Subject: Re: [gmx-users] Capping residues
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sai Pooja wrote:
> >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.
> >I was trying to use ACE for acetyl but it is not recognized by
> >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.
> >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
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