[gmx-users] Query regarding phosphothreonine parameters

[nikhil damle]

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 <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
> 
> ------------------------------------------------------------------------
> See the Web's breaking stories, chosen by people like you. Check out Yahoo! Buzz <http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/>.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- ========================================

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

========================================
_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php



      Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090907/afd8c7d1/attachment.html>