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

[Antoine Delmotte]

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?

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
>>
>>
>>
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>