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

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Thu Jun 14 2012 - 08:18:08 CDT

My apologies - I meant to write leap / xleap but somehow got the
programs switched in my head. Thanks for catching the error.

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 Thu, Jun 14, 2012 at 2:41 AM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:
> Hi,
>
>> -----Ursprüngliche 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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