Re: COOH patch?

From: MIke S (vmd.namd_at_gmail.com)
Date: Mon Sep 01 2008 - 18:46:36 CDT

Thank you for the useful information Thomas.

I'm currently using the toplogy files from Alex Mackerell's website, which
appear to be for CHARMM version c31b1. Am I right in assuming that I'll
need to get a license for CHARMM to access the parameter and topology files
you were referring to, or are these files accessible through another
Professor's website?

Best regards,

Mike

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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