[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 5 19:23:40 CET 2010

Antoine Delmotte wrote:
> Dear gmx-users,
> I would like to simulate the CDK9 protein (3BLH in PDB), but there is 
> one residue (TPO, phosphothreonine), which Gromacs does not recognise.
> I found the PRODRG website as well as force field parameters for TPO for 
> the Gromos96.1 force field. However, I would like to use the OPLS-AA 
> force field. I therefore need a topology file for this force field, 
> which cannot be provided by PRODRG (only useful for united atoms force 
> fields).
> Does anyone have an idea about where I could get the phosphothreonine 
> itp file for OPLS force field?

Search the literature to see if anyone has published parameters for it.

> Otherwise, could someone give me clues or the link to a good tutorial 
> about how to create this itp file myself?

That's what Chapter 5 of the manual is for, provided you have reliable 
parameters (see below).

> Molecular dynamics is something completely new for me so, sorry if I ask 
> stupid questions. It also seems I am not the first one to have this 
> problem but I could not find any solution on the archive of the mailing 
> list.

If MD is completely new to you, and you are unable to find previously published 
and validated parameters, the parameterization of a new species is likely not a 
suitable task.  Parameterization is an expert topic, and it can take many months 
or years to develop reliable parameters, even if you know what you are doing at 
the very start.  Be forewarned:



> I thank you in advance.
> Best regards,
> Antoine
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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


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