From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 01 2006 - 18:01:15 CDT

Hi,
  Did you send us the same sphere.pqr you loaded below? I'm not getting
any of the bonding errors your message below was showing.
If you can upload the DX file to the VMD Public project area on BioCoRE, I'd
like to have a look:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Most likely you just need to create an Isosurface representation after
the data is loaded. Also, although the APBS home page directs people
to use their my_functions.tcl script for loading DX files (in particular
for older versions of VMD), the built-in DX reader plugin in VMD 1.8.4
is MUCH faster. (just load the DX file using the File menu as for other
files...)

To keep things simple to start with, try loading just the DX file into
VMD (using the built-in DX reader, rather than the load_pot script routine..)
and see if you see the potential surface. Once you get that far, we can
move on to the next questions..

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 01, 2006 at 06:34:04PM -0400, Vyom Sharma wrote:
> I am getting a very strange problem for quite sometime now.
> I use a "PQR" file that i generate and run it on APBS to give me the
> potential data.
> VMD is able to show the molecule nicely but it is not able to visualize
> the potential data at all. Infact it does not show anything when I try
> to load the potential data.
>
> I am using the "my_functions" script to sort and load the potential
> data into VMD.
> Also I am attaching the "PQR" file (I can send the "pot.dx" file which
> contains the potential data , if required- its 27 MB big)
>
> While loading the potential using "load_pot" command, I get these
> messages:
>
> ---------------------
> nfo) VMD for MACOSX, version 1.8.4 (April 17, 2006)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 1 CPU detected.
> Info) OpenGL renderer: ATI Radeon 9200 OpenGL Engine
> Info) Features: STENCIL MTX
> Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (6)
> vmd > source my_functions
> vmd > load_pot
> Info) Using plugin pdb for structure file sphere.pqr
> Info) Using plugin pdb for coordinates from file sphere.pqr
> Info) Determining bond structure from distance search ...
> ERROR) MolAtom 131: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 173: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 285: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 423: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 79: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 310: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 147: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 475: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 140: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 331: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 292: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 256: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 177: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 196: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 222: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 263: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 210: Exceeded maximum number of bonds (8).
> ERROR) MolAtom 110: Exceeded maximum number of bonds (8).
> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom
> coordinates are in the wrong units?
> ERROR) BaseMolecule: Silencing bonding error messages.
> Info) Finished with coordinate file sphere.pqr.
> Info) Analyzing structure ...
> Info) Atoms: 501
> Info) Bonds: 1112
> Info) Residues: 53
> Info) Waters: 0
> ---------------------------------------
>
>
> I would immensely appreciate any repsonse.
>
> Thanks
> Vyom
>

>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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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