nikhil damle wrote:
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 ??
There are plenty of things that could have gone wrong. I would not necessarily
take the gamma-PO4 from ATP for phosphothreonine, however. There are lots of
charge transfer issues in ATP that are not present in phosphothreonine. Please
read the reference I cited, it is a validated parameter set.
If you're getting LINCS warnings, the first steps are whether or not the
minimization and equilibration schemes you have used are sufficient. If you can
describe what you've done, the results of EM, etc (including .mdp files), then
we can better diagnose.
But I would start over with published, validated parameters :)
-Justin
I hope i have made myself clear this time regarding the problem.
regards,
Nikhil
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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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========================================
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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