From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 30 2012 - 10:34:05 CST
I assume you're referring to paratool? You should give fftk a try:
Note that it's still under development, but a new, more complete release
should be out soon. It requires access to Gaussian, but handles the setup
and analysis of the files.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Dr. Eddie
Sent: Friday, November 30, 2012 9:10 AM
Subject: namd-l: Force field Parametrization
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.
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