[gmx-users] Capping residues

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 1 01:57:11 CEST 2010

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.

> 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.



> Regards
> Pooja
> -- 
> Quaerendo Invenietis-Seek and you shall discover.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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