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.
--
========================================
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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