VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2005 - 16:08:13 CDT

Vivek,
  I've tracked down the problem to a vertex index of 0 (-1 when it gets
to VMD) in the SRF file. My belief was previously that GRASP produced
files with 1-based indices, and indeed this is the first surface file
I've seen with a zero-valued vertex index, so I'm not sure what that means.
In any case, it should be easy to fix or workaround. I should have a new
graspplugin ready in a day or so.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 16, 2005 at 06:38:33PM +0300, vivek sharma wrote:
> Hello John,
>
> Atleast the srf file loads finely in GRASP, but doesnot work in VMD. The
> files are attached. Thanks very much for the help.
>
> br,
>
> Vivek
>
> Quoting John Stone <johns_at_ks.uiuc.edu>:
>
> >
> > Vivek,
> > It sounds like your grid/srf files may not be compatible with our
> > readers for those formats. Can you send me a copy of the two files that
> > fail to load so I can take a look at them?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Sep 16, 2005 at 09:52:45AM +0300, vivek sharma wrote:
> > > Hello John,
> > >
> > > Situation is:
> > >
> > > I am loading a pdb in VMD (using 1.8.3 both Win and Linux), it goes
> > fine.
> > > Now, I would like to load the *.grd (binary potential map file from
> > > Insight/Delphi calc.) and I am doing it by selecting the molecule in
> > VMD
> > > Main (already loaded pdb) and using 'Load Data into Molecule'. BUt, it
> >
> > > doesnot go fine and error in console is:
> > >
> > > Improperly formatted file header: uplbl
> > > ERROR) Unable to open file with plugin of type grd
> > >
> > > Actually, I searched the mailing list with this and found few emails,
> > but
> > > couldn't understand how to get it done. Any help will be great.
> > >
> > > Secondly, I also have a *.srf (GRASP surface file generated by
> > > Insight/Delphi calculation), when I load it in VMD by selecting file
> > > type 'grasp' from Molecule file browser, VMD does something for
> > sometime
> > > but dies with a core dump.
> > >
> > > Am I doing the stuff right or is there anything wrong? ANy suggestions
> >
> > > will be great.
> > >
> > > Thanks in advance,
> > >
> > > br,
> > >
> > > Vivek
> > >
> > >
> > > --
> > > VIVEK SHARMA
> > > HBG BI
> > > "Better to understand a little than to misunderstand a lot." (?)
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> --
> VIVEK SHARMA
> HBG BI
> "Better to understand a little than to misunderstand a lot." (?) 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078