VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Feb 06 2008 - 10:47:56 CST

On Wed, 6 Feb 2008, C L Freeman wrote:

CF> Hello,

colin,

CF> I'm currently trying to use vmd to visualise a system composed of
CF> some 28,000 calcite atoms with a protein/water mix of some 75,000

   calcite "atoms"?

CF> atoms so a total system of 103,000 atoms. vmd returns an error when
CF> I try and load the pdb file to view this structure I get an error
CF> claiming some of my atoms have exceeded the maximum number of bonds.

the way to get around this would be to provide a file with the
bonding information (or recompile VMD to support more bonds).
the warning about excessive bonds usually means that some atoms
are close to overlapping. has your system been run as an MD or
geometry optimization already?

CF> Now I know this is not the case as I can load the two structures
CF> indepently with no problems as none of the atoms have more than 4
CF> bonds. If I try to load one structure and then the other I then get
CF> the error:
CF>
CF> "Incorrect number of atoms (the number of atoms in the file)"

you have to understand the logic of "molecules" and "frames" in VMD.
it is not always obvious.

a "molecule" in VMD is one structure, usually defined by a topology
file like .psf or .parmtop (which can actually consist of many
molecules). a "frame" is a set of coordinates for this "molecule".
for loading .pdb (or .xyz or similar) files, VMD considers them
to contain both and it will try to guess the missing structure
information (e.g. bonds) based on internal heuristics.
if you load a second file into an existing "molecule" VMD assumes
that you want to load another frame (i.e. only coordinates) into
an existing molecules and for that to work the second file has
to contain the exact same number of coordinates. the test for this
is an internal safety check. so the only way to have a merged
structure is combinding the two .pdb files and loading them
as one. so you should check of unusually close atoms and generally
check your combined file. if you still are convinced that the
file is 100% correct, please upload it to the VMD public biocore
project (instructions are on the VMD homepage) so that VMD
developers can have a look at it.

hope that helps.

cheers,
   axel.

CF>
CF> This suggests to me that there may be some issue with regard to the number of
CF> atoms allowed? Is there a parameter I can change to account for this?
CF>
CF> Cheers
CF> Colin
CF> 

-- 
=======================================================================
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
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If you make something idiot-proof, the universe creates a better idiot.