Re: COOH patch?

From: MIke S (vmd.namd_at_gmail.com)
Date: Wed Sep 17 2008 - 11:39:25 CDT

If anyone else needs the neutral patches for the N and C terminus you can
now access them thanks to Alex MacKerell. An updated topology file is now
available on his website.

On Sat, Aug 30, 2008 at 8:08 PM, Thomas Gaillard <
gaillard_at_chimie.u-strasbg.fr> wrote:

> 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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