Re: question about using Amber force field in namd

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jun 02 2004 - 16:31:48 CDT

Hello
As stated in the web page you can use a pdb file if you use the
coordinates keyword.

Brian

On Wed, 2 Jun 2004 jz7_at_duke.edu wrote:

> Thanks! Then how to generate the crd file? Is it the same as coordinate
> file (.pdb)?
>
> On Wed, 2 Jun 2004, Brian Bennion wrote:
>
> >
> > Hello
> > parmfile AMBER format PARM file
> > Acceptable Values: UNIX filename
> > Description: This file contains complete topology and parameter
> > information of the system.
> >
> > So, you don't need a psf file, just the the amber formatted parm file and
> > an amber crd file.
> >
> > Brian
> >
> >
> > On Wed, 2 Jun 2004 jz7_at_duke.edu wrote:
> >
> > > Thanks!
> > >
> > > 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!
> > >
> > > Best,
> > > Jeny
> > >
> > > On Wed, 2 Jun 2004, Brian Bennion wrote:
> > >
> > > >
> > > > Hello Jeny,
> > > >
> > > > What part of this page has you stuck?
> > > >
> > > > http://www.ks.uiuc.edu/Research/namd/current/ug/node15.html
> > > >
> > > > 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 jz7_at_duke.edu 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 bennion1_at_llnl.gov **
> > > > **7000 East Avenue phone: (925) 422-5722 **
> > > > **Livermore, CA 94550 fax: (925) 424-6605 **
> > > > *****************************************************************
> > > >
> > > >
> > >
> >
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 424-6605 **
> > *****************************************************************
> >
> >
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************

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