[gmx-users] Terminal group patching

[Justin Lemkul]

On 4/20/17 2:26 PM, Alex Mathew wrote:
> Hi,
>
> 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
> CTER
> CT1
> CT2
> CT3
> NONE
>
> 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

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

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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