[gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
antoinedelmotte at hotmail.com
Sat Feb 6 17:05:22 CET 2010
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?
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
>> I thank you in advance.
>> Best regards,
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