VMD-L Mailing List

From: Yogesh Aher (aher.yogesh_at_gmail.com)
Date: Mon Jul 20 2009 - 07:22:21 CDT

Hello Alex,

I tried the 2nd safe option. As .prmcrd couldn't load automatically. so I
just opened .prmtop file alongwith the solvated pdb file generated in last
step on tleap. Then chose "protein and noh" option and the resulting
structure saved with option "save co-ordinates".
But when I checked with another visualization software, it seems that only
protein is saved without ligand. What may be the problem or mistake I made?
I tried it several times, but no success.

Look forward to hear from you!

Sincerely,
Y.

On Fri, Jul 17, 2009 at 5:14 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu
> wrote:

> 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.
>
>