Re: COOH patch?

From: Thomas Gaillard (gaillard_at_chimie.u-strasbg.fr)
Date: Sat Aug 30 2008 - 19:08:41 CDT

On Sat, Aug 30, 2008 at 06:24:20PM -0400, MIke S wrote :
> Hello,
>
> Could anyone suggest a way to create a protonated C-terminus for a protein?
> Do I need to create a new entry in the topology file based on existing
> ones? If so any suggestions on the best approach?
>
> I've noticed a similar unanswered post from a few years ago (
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2980.html). Also,
> the following post suggested acetylating or methylating the terminus, but I
> would prefer to protonate the carboxyl group instead.
> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7055.html)

Hello Mike, what you are looking for has been added to CHARMM topology
and parameter files since the c35a2 version :

http://www.charmm.org/html/package/changelogs/c35log.html#SECTION2

..

2.12 Force Field Parameter Updates
    Developers : Alex D. MacKerell
    Email Address : alex_at_outerbanks.umaryland.edu
    Institution : University of Maryland, School of Pharmacy
    Date : December 31, 2007

..

  3) Proteins: Neutral N- and C-terminal patches added: NNEU and CNEU.

Regards,

-- 
Dr. Thomas Gaillard
Laboratoire de Biophysicochimie Moléculaire
Institut de Chimie LC3 - UMR 7177
Université Louis Pasteur
4 rue Blaise Pascal
F-67000 Strasbourg
phone: +33 (0)390 241 493
fax: +33 (0)390 241 490
mail: gaillard_at_chimie.u-strasbg.fr
web: http://lbm.u-strasbg.fr/gaillard

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