[gmx-users] amidated C-terminal residue of peptide

[Justin Lemkul]

Please don't reply to the entire digest.

On 5/28/16 2:09 AM, kamakshi sikka wrote:
> Dear Justin,
>
>
> Charmm GUI created the topology file for the membrane only..I am asking for
> C-terminal amidated peptide topology file. pdb2gmx command does not give
> topology file here because of C-terminal amide residue which is missing in
> the residue database. Please help.
>

CHARMM-GUI can build the entire membrane-protein complex, you just need to carry 
out a few more steps.

Otherwise, the patching is simple.  Choose the CT2 C-terminus type if using our 
CHARMM36 port.  That builds a C-terminal amide.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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