[gmx-users] Query regarding phosphothreonine parameters

[Justin A. Lemkul]

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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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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-- 
========================================

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

========================================