[gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Mar 28 10:38:54 CEST 2007

Hi Fulya,

In addition to Mark's comments, if you have a friend who has the
proper background for such parameterization he/she will know what to
do and I don't need to describe the process. The basic thing is that
if you're a novice with MD, it's best to first take the paths well
walked by others, before starting new trails (in terms of
methodology/parameters; I don't want to suggest to repeat projects
from others, that's basically what tutorials are for, but I would
advice to use proteins/dna with no strings attached).

Regarding the mail server, the first two mails only arrived as
forwarded mails, with a lot of junk around the main question (which
makes reading less convenient).



On 3/28/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> fulya caglar wrote:
> >     Hi Tsjerk,
> >     Do you know how can I add parameters for sulfite bound?You are right
> > I have little experience in this field but maybe one of my friends can
> > do this.I would be very grateful if you can explain  parameterization
> > briefly.
> It's an involved process, which varies considerably depending on the
> force field you're trying to extend. You should start by reading the
> paper that describes the parameterization of the force field you're
> trying to extend, and then thinking hard about how you can follow a
> similar process to get parameters that are consistent.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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