[gmx-users] Capping residues

[Justin A. Lemkul]

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.

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

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

-- 
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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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