From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Jun 02 2004 - 16:21:21 CDT
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 **
*****************************************************************
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