From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Tue Jun 12 2012 - 17:49:46 CDT
Hi Scott,
You have two options:
1) Prepare prmtop (amber parameter+topology) and coordinate files for
the system using Antechamber (see www.ambermd.org). Then use these in
namd (see http://www.ks.uiuc.edu/Research/namd/2.9/ug/node13.html).
2) Use the CHARMM-formatted amber topology file in the ./non_charmm
directory of the charmm force field distribution (from
http://mackerell.umaryland.edu/CHARMM_ff_params.html) to generate pdb
+ psf files. Then use these pdb+psf files along with the
CHARMM-formatted amber parameter file from the ./non_charmm directory
in your namd calculation.
There are some minor barriers to overcome with either method (related
mostly to different amino acid and atom naming conventions or
file-format issues). Also note the change in 1-4scaljng in namd when
using the amber force field (0.833333 instead of 1.0).
Cheers,
Johan
------------------------------------------------------------------------------------------------------
Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
Ph.D. Candidate
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Tue, Jun 12, 2012 at 5:49 PM, scott davis <scottcd13_at_gmail.com> wrote:
> Hello,
> I have looked through the tutorial and the previous messages and found the
> answers received a little hard to digest.
> I am trying to figure out how to run a simulation in NAMD using amber force
> field. I have read that different input files are needed then psf/pdb. I
> understand that yet have not been able to find a gui or utility to feed the
> psf/pdb into that will either make or allow me to make the files needed.
> Also if anyone has a sample configuration file so I have something to work
> off from. I am somewhat new to NAMD/ VMD and not very familiar with all of
> the features.
>
> Thank you,
>
> Scott Davis
>
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