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

[Yang Ye]

fulya caglar wrote:
> Hi Tsjerk,
> Thanks for your help.You're right about "taking paths well walked by 
> others,before starting new trails" but I have to do this simulation 
> for my study:(
Then do it in a right way. Hurry up!
> Thanks very much for your suggestions again.
> Sincerely
> Fulya
> */Tsjerk Wassenaar <tsjerkw at gmail.com>/* wrote:
>
>     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).
>
>     Best,
>
>     Tsjerk
>
>     On 3/28/07, Mark Abraham 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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