RE: vmd-l: PSFGEN problem

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Oct 11 2004 - 11:19:56 CDT

HI Matt,

I am not sure what is going on with the 'readpdb' command in vmd.

But it seems you found a work around.
Let me try and understand the problem better. With the small box of water
that you created in VMD you need a psf file that reflects that topology?

If that is the case, then one doesn't need 'readpdb' really.

Instead, make and atomselection within vmd that reflects the smaller
system. write that out with "atomselectXX writepdb test.pdb"

Then load that pdb file into psfgen segments, one for protein, the other
segment for water. employ the coordpdb option and then writepdb and
writepsf the current segments.

Maybe you did this already, I am not familiar with the BPTI tutorial.

Regards
Brian

On Sat, 9 Oct 2004, Matthew Cooper wrote:

> Hey Brian,
>
> Hi again - I appreciate your help.
>
> I can build the box, but our computational resources are very small at the
> moment so I need to destroy most of the box leaving only a thin layer of
> solvent molecules around the protein - using the -t command builds a huge
> box of solvent.
>
> So I cut it down using tkcon commands, but the problem arose when I tried to
> get a new .psf file with the .pdb file I generated. The psfgen user guide
> has a tutorial that says to use the command 'readpdb' - it is this command
> that I cannot figure out. If I go into tckon and try to find all available
> commands that start with 'r' I get (from vmd 1.8.2):
>
> Main console display active (Tcl8.4.1 / Tk8.4.1)
> () 1 % r
> ambiguous command name "r": radiobutton raise ramaplot rawtimestep read
> readpsf regenerate regexp regsub rename render resetpsf residue return
> rmsdtool_tk_cb rock rotate rotmat
>
> from the psfgen user guide:
>
> 2.2 Deleting unwanted atoms
> # Load a pdb and psf file into both psfgen and VMD.
> resetpsf
> readpsf myfile.psf
> readpdb myfile.pdb
> mol load psf myfile.psf pdb myfile.pdb
>
> I figured it out eventually (using the BPTI method in the user guide) but I
> don't know if you can help me figure out what is going on with the psfgen
> commands - the instructions they laid out would have been great if I could
> have used the 'readpdb' command.
>
> Thanks,
>
> Matt
>
> -----Original Message-----
> From: Brian Bennion [mailto:brian_at_youkai.llnl.gov]
> Sent: October 8, 2004 11:17 PM
> To: Matthew Cooper
> Subject: RE: vmd-l: PSFGEN problem
>
> Hi Matt,
>
> I guess I misunderstood how you built your ura2 residue. Anyway, the
> solvent box can be built by the solvate command within vmd
>
> solvate file.psf file.pdb -t 10 -b 1.67
>
> will build a 10 angstrom water box around your protein and keep waters
> from being placed less than 1.67 angstroms from the surface of the
> protein.
>
> type solvate in the vmd console for more options.
>
> Regards
> Brian
>
>
> On Fri, 8 Oct 2004, Matthew Cooper wrote:
>
> > Hey Brian,
> >
> > I did end up aliasing from URA to URA2 and it worked fine.
> >
> > The problem seemed to be with VMD not wanted to go to a different
> directory.
> > When I changed the .pgn file so that all the called files were in the same
> > directory as the .pgn file there were no problems.
> >
> > What is weird is that the psfgen user guide says that, in order to build a
> > proper size solvent box, you have to use the command "readpdb" but that
> does
> > not seem to be an option within the VMD tkcon window - am I missing
> > something?
> >
> > Thanks,
> >
> > Matt
> >
> > -----Original Message-----
> > From: Brian Bennion [mailto:brian_at_youkai.llnl.gov]
> > Sent: October 8, 2004 7:58 PM
> > To: mdcooper
> > Cc: vmd-l
> > Subject: Re: vmd-l: PSFGEN problem
> >
> > Hi Matt
> >
> > First you can't alias the URA to URA2, if URA is already a known residue
> > in the topology file.
> > If that is what you are actually doing?
> > The memory error is caused by psfgen/vmd, most likely because of the
> > previous comment.
> >
> >
> > Can you give some more information?
> > OS?
> > vmd version?
> > psfgen version? compiled or downloaded with vmd
> >
> > Any other apps running at the same time?
> >
> > Regards
> > Brian
> >
> >
> > On Fri, 8 Oct 2004, mdcooper wrote:
> >
> > > I am trying to build a psf file for a complex with URA, except it is a
> URA
> > > molecule with an extra oxygen than the one provided in CHARMm so I have
> > built
> > > URA2.
> > >
> > > I am aliasing URA to URA2 in the .pgn file.
> > >
> > > WHen I try to run the .pgn file it gets as far as extracting the 238
> > residues
> > > and then, apparently, reference bad memory and fails (ie the failure
> > occurs
> > > outside of VMD). This is the same thing that happens when I tried to
> build
> > a
> > > psf file with a molecule that contained hydrogens.
> > >
> > > Can anyone help - it is driving me nutty.
> > >
> > > thanks,
> > >
> > > matt
> > >
> > > ATOM 1806 CG2 ILE A 237 75.765 42.905 46.179 1.00 54.08
> > > ATOM 1807 CD1 ILE A 237 75.871 42.087 42.450 1.00 53.68
> > > ATOM 1808 N1 URA A 238 62.024 57.956 28.031 1.00 14.18
> > > ATOM 1809 C2 URA A 238 61.074 57.866 29.056 1.00 15.27
> > >
> > >
> >
> > *****************************************************************
> > **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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