[gmx-users] Terminal group patching
jalemkul at vt.edu
Thu Apr 20 20:30:01 CEST 2017
On 4/20/17 2:26 PM, Alex Mathew wrote:
> How to find the in the most realistic way?
> When i tried to build a protein-membrane system using charmm-gui there were
> two options
> First is GLYP and ACE and for last there was options like
> which one i should select?
> How do i know which one
If you're working with CHARMM and you aren't familiar with what those are, go
get the CHARMM force field files
(http://mackerell.umaryland.edu/charmm_ff.shtml#charmm) and look at
top_all36_prot.rtf (search down for PRES) and you will see the chemical
structures and a description of each patch.
You make your decision based on the actual chemistry of the system. The choice
of GLYP vs. ACE indicates you have a Gly at the N-terminus and GLYP is the
default choice (free -NH3+ as most proteins will have). If your protein is, for
instance, a fragment of a larger protein such that the N-terminus is artificial,
typically these are capped (acetylated) to avoid spurious end effects. Likewise
with the C-terminus.
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
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