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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