[gmx-users] Capping residues

[Mark Abraham]

----- 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:
> >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
> 
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