From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 20 2009 - 08:54:41 CDT

On Mon, 2009-07-20 at 14:22 +0200, Yogesh Aher wrote:
> Hello Alex,
>
> I tried the 2nd safe option. As .prmcrd couldn't load automatically.

if it doesn't load automatically, you have to specify
the file type explicitly. the automatic loading only
works for certain file name extensions. sometimes people
use different naming conventions, sometimes a certain
extension is already taken by a different plugin.

this is a basic VMD issue. have a closer look at
the VMD user's guide and the VMD tutorials.

> 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?

the mistake is that you assume that everything works automatically.
option 2 means that you have to build your whole topology again
with psfgen. if you have a protein and a ligand, you have to split
them into separate segments, build the topology, neutralize (if needed),
solvate etc. etc. the whole ball of wax. it is documented in the
psfgen user's guide and the topology tutorials. i said it would be
more work.

at this point, however, i'm wondering what great software it is you
want to that you cannot use NAMD, for example. as NAMD does understand
amber format topology files and is a pretty good and fast MD code.

cheers,
   axel.

> 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.
>
>
>

-- 
=======================================================================
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.