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

[Justin A. Lemkul]

Antoine Delmotte wrote:
> 
> Thank you very much for your quick response, Justin. I guess I need a 
> little bit more practise to make the parametrization myself. Do you have 
> any clues on where I could find published parameters? Are there 
> databases for this or something similar?
> 

Literature searching is your best bet.  But as far as I know, there is no 
database of previously-published parameters.  Understanding the intrinsics of 
the force field (the original derivation and subsequent improvements) will be 
the most useful for you to understand the intrinsics of the force field.

If you're dead set on using OPLS, then you probably have (a lot) of work cut out 
for you.  Parameters for phosphorylated Ser, Thr, and Tyr for Gromos96 43a1 were 
published some time ago.

-Justin

> Regards,
> 
> Antoine
> 
> Le 5/02/2010 18:23, Justin A. Lemkul a écrit :
>>
>>
>> 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:
>>
>> http://www.gromacs.org/Documentation/How-tos/Parameterization
>>
>> -Justin
>>
>>> I thank you in advance.
>>>
>>> Best regards,
>>>
>>> Antoine
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> Hotmail : une messagerie fiable avec la protection anti-spam 
>>> performante de Microsoft Inscrivez-vous 
>>> <https://signup.live.com/signup.aspx?id=60969>
>>>
>>
> 
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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