VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 17 2009 - 10:14:24 CDT

On Fri, 2009-07-17 at 17:03 +0200, Yogesh Aher wrote:
> Dear Alex,
>
> Thank you very much for your kind reply.
> I read the psfgen tutorials and also searched archieves. What I think
> is the need is - converting .prmtop and .prmcrd files into .psf
> and .pdb format respectively. I am sorry but I couldn't find such
> thing!

there are two options. one is more work but more likely to succeed
than the other.

a) the "cheap" one. download the latest VMD beta version. load your
   prmtop file and save it as a .psf file. then load the .crd file
   "into" the molecule and save it as .pdb and then cross your
   fingers and see if the result works.

b) the "safe" one. load .prmtop and .crd into vmd, make a selection
   with the protein only and without hydrogens and save that as .pdb
   file. then build a topology from it as usual with psfgen.

good luck,

     axel.

ps.: please always keep the mailing list in cc, so that other people
that may have the same problem, can see the resolution as well.

> Will you please give me a little insight into it.
>
> Thanking you,
>
> Yogesh
>
> On Fri, Jul 17, 2009 at 2:23 PM, Axel Kohlmeyer
> <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> On Fri, 2009-07-17 at 11:34 +0200, Yogesh Aher wrote:
> > Dear Amber users,
> >
> > I searched the past archieves but couldn't find the relevant
> solution,
> > so writing it again.
> > I am facing bit complicated problem currently. We have some
> new MD
> > software, but it is not accepting .prmtop and .prmcrd files
> as input
> > for running the simulation.
> > Instead, it says:
> >
> > "To allow your AMBER-simulated systems to be run,
> coordinates and
> > structure files must be regenerated using VMD and the
> AMBER topology
> > file in CHARMM format, as all input files must be in CHARMM
> format."
> >
> > Anyone has any idea how to deal with such case?
>
>
> yep. check out the psfgen tutorials. all you'd need is the
> corresponding AMBER parameter and topology files in CHARMM
> format. they exist in several versions, so you may want to
> check out the NAMD and VMD mailing archives or the web in
> general for them.
>
> cheers,
> axel.
>
> >
> > Thanking you,
> >
> > Sincerely,
> > Yogesh
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of
> Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a
> better idiot.
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.