RE: question about using Amber force field in namd

From: Kamp, Marc vander (
Date: Thu Jun 03 2004 - 01:19:12 CDT

Hello Jenny and others,
After the e-mails from Brian I think you know already a lot more, but as I gathered from your e-mail you might still have a problem (which was already shortly discussed about a week ago after a posted question from Ed O'Brien):
Next to the paramter-file (the .dat file) you'll need an AMBER topology file, which is more or less the AMBER equivalence of a pdf-file. This means that you have to create one for the system (protein + DNA strand) you are working with. Creating such an parmtop-file (as AMBER topology files are often called) can be done with tleap, an AMBER program which you can also get from the free NAB-distribution (from the Case-group, ) if you have no access to AMBER. Hope this helps.
I'm trying to do the same on the moment. I've installed tleap (from the NAB distribution) and it is working. The problem I'm currently facing is that I can't get tleap to write out parmtop-files of a solvated system, because it does not recognize the water-molecules / has no parameters for them. I'll try to solve this (tips anyone?) and if I don't succeed, post my question (more detailed) on the AMBER mailing list.

        -----Oorspronkelijk bericht-----
        Van: namens
        Verzonden: wo 2-6-2004 23:13
        Aan: Brian Bennion
        Onderwerp: Re: namd-l: question about using Amber force field in namd

        I have parm*.dat file. But first, how to generate the psf structure file?
        The way I did in Charmm ff is write a tcl file, which specify the topology
        file and the gragments. But when using Amber, what command lines should I
        add? What is the corresponding topology file? (Is it the ".inp" file in
        Amber force field? But it has seperate file for protein and DNA. How can I
        include both of them?)
        Thanks a lot!
        On Wed, 2 Jun 2004, Brian Bennion wrote:
> Hello Jeny,
> What part of this page has you stuck?
> if you are needing to use the amber functions of NAMD then you must have a
> an amber parm file laying around. This rest is as stated on the above web
> page.
> Brian
> On Wed, 2 Jun 2004 wrote:
> > Dear all,
> >
> > I am trying to use Amber force field in NAMD. After reading the User's
> > manual, I am still not quite clear about how to do that. So I am
> > wondering if there are some sample inputs for generating PSF file,
> > minimization, etc. I have some experience on using NAMD with Charmm
> > force field. What's the difference between using Amber and using Charmm
> > in NAMD?
> >
> > Thanks a lot!
> >
> > Sincerely,
> > Jeny
> >
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************

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