From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Fri Nov 30 2012 - 09:39:49 CST
Hi,
You can use GAFF for your ligand together with an Amber ff for your protein
or membrane. There is a tutorial on ACPYPE website for this:
http://code.google.com/p/acpype/wiki/TutorialNAMD
If you want to calculate partial charges and optimized geometry with a QM
method without learning to operate the respective program, you can use the
R.E.D. server:
http://q4md-forcefieldtools.org/REDS/
ACPYPE takes as an input R.E.D server output and creates the topologies
automatically for GROMACS. I'm not sure if it does it for NAMD though. If
not, just change the partial charges by hand, or something like that. It
shouldn't be too hard I guess...
HTH,
Thomas
On 30 November 2012 17:09, Dr. Eddie <eackad_at_gmail.com> wrote:
> Hello all,
> I'd like to include an inhibitor in my namd simulation. I see vmd has a
> tool to create the parameter file needed, although everything must be
> entered manually (and then you hope you haven't made a mistake). I've seen
> the Spartan tutorial which is nice but that's not free software. The
> antechamber requires Gaussian (and thus learning how to use Gaussian). Does
> anyone have any experience generating a force field parameter file using
> free software and what would be the simplest route for doing this? (I'm not
> expecting it to be trivial, I just don't want to run a marathon if there is
> a shortcut).
>
> I appreciate any help. I kow this isn't exactly namd specific but I need
> the resultant file to be usable by namd and thus other methods which may be
> automatic are not of use if namd can't use them as input.
>
> thanks,
> Eddie
>
>
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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