AW: Trying to run a setup with amber force field in NAMD

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jun 14 2012 - 01:41:15 CDT

Hi,

> -----Urspr√ľngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von johan strumpfer
> Gesendet: Mittwoch, 13. Juni 2012 00:50
> An: scott davis
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: Trying to run a setup with amber force field in
> NAMD
>
> 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).

Careful here, antechamber is a tool for parameterization of new residues. To set up a system one uses the ambertools leap or xleap.

Norman

>
> 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
> -----------------------------------------------------------------------
> -------------------------------
>
>
> 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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