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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
