Hi,
Thanks a lot for the suggestions. I have to simulate a system containing
phosphothreonine; for which i need to include this residue in .rtp file of the
forcefield which i m using (ffG43a1). For this purpose i require the charges
and other values of the phosphate grp attached to threonine. I tried to imitate
OPO4- from the gamma-Phosphate of ATP in ffG43a1 and tried to simulate the
system. But bond constraints warning arises. So i thought my values are
probably wrong. So now the question is how will i check if my values are
incorrect or not ? Where will i get parameters for phosphothreonine residue ??
I hope i have made myself clear this time regarding the problem.
regards,
Nikhil
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Monday, 7 September, 2009 3:55:58 PM
Subject: Re: [gmx-users] Query regarding phosphothreonine parameters
nikhil damle wrote:
>
> Hello,
>
> Where will I get Phosphothreonine parameters ? I have tried to incorporate
> gamma-Phosphate parameters from ATP in the threonine residue but in vain.
>
The answer for parameterization is always the same:
http://oldwiki.gromacs.org/index.php/Parameterization
There are parameters out there for phosphorylated amino acids, compatible with
ffG43a1:
Hansson, Nordulund, and Aqvist. (1997) J. Mol. Biol. 265: 118-127.
But simply saying you've tried and failed is useless. If you describe which
force field you're trying to use, what you've done, and what the actual problem
is, you're likely to inspire someone to help you.
-Justin
> regards,
> Nikhil
>
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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