VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Feb 07 2008 - 05:58:14 CST

On Thu, 7 Feb 2008, C L Freeman wrote:

colin,

CF> Thanks for your help Axel.

[...]

CF> earlier case the atom numbers would have been less than 100,000.
CF> The problem stems from my formatting of the pdb file. In my problem
CF> file I have:
CF>
CF> ATOM 100000 etc.
CF>
CF> clearly vmd can read a 6 digit atom number but it expects this atom
CF> number to start only 1 space after ATOM not 2. Persumably it has
CF> been coded with dividing lines into specfic numbers of characters
CF> as each term?

yes. please look up the PDB standard. this _has_ to be done,
since the PDB format is based on fortran fixed format, i.e.
each field in a line has a fixed set of columns. if you "shift"
those, part of the coordinates will not be read. if you generate
coordinates more often, it might be better to switch to a format,
where this restriction is not present.

cheers,
   axel.

CF>
CF> ATOM 100000 etc.
CF>
CF> I could visualise everything fine.
CF>
CF> Thanks again for your help
CF> Colin
CF>
CF>
CF> Quoting Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>:
CF>
CF> > On Wed, 6 Feb 2008, C L Freeman wrote:
CF> >
CF> > CF> Hello,
CF> >
CF> > colin,
CF> >
CF> > CF> I'm currently trying to use vmd to visualise a system composed of
CF> > CF> some 28,000 calcite atoms with a protein/water mix of some 75,000
CF> >
CF> > calcite "atoms"?
CF> >
CF> > CF> atoms so a total system of 103,000 atoms. vmd returns an error when
CF> > CF> I try and load the pdb file to view this structure I get an error
CF> > CF> claiming some of my atoms have exceeded the maximum number of bonds.
CF> >
CF> > the way to get around this would be to provide a file with the
CF> > bonding information (or recompile VMD to support more bonds).
CF> > the warning about excessive bonds usually means that some atoms
CF> > are close to overlapping. has your system been run as an MD or
CF> > geometry optimization already?
CF> >
CF> > CF> Now I know this is not the case as I can load the two structures
CF> > CF> indepently with no problems as none of the atoms have more than 4
CF> > CF> bonds. If I try to load one structure and then the other I then get
CF> > CF> the error:
CF> > CF>
CF> > CF> "Incorrect number of atoms (the number of atoms in the file)"
CF> >
CF> > you have to understand the logic of "molecules" and "frames" in VMD.
CF> > it is not always obvious.
CF> >
CF> > a "molecule" in VMD is one structure, usually defined by a topology
CF> > file like .psf or .parmtop (which can actually consist of many
CF> > molecules). a "frame" is a set of coordinates for this "molecule".
CF> > for loading .pdb (or .xyz or similar) files, VMD considers them
CF> > to contain both and it will try to guess the missing structure
CF> > information (e.g. bonds) based on internal heuristics.
CF> > if you load a second file into an existing "molecule" VMD assumes
CF> > that you want to load another frame (i.e. only coordinates) into
CF> > an existing molecules and for that to work the second file has
CF> > to contain the exact same number of coordinates. the test for this
CF> > is an internal safety check. so the only way to have a merged
CF> > structure is combinding the two .pdb files and loading them
CF> > as one. so you should check of unusually close atoms and generally
CF> > check your combined file. if you still are convinced that the
CF> > file is 100% correct, please upload it to the VMD public biocore
CF> > project (instructions are on the VMD homepage) so that VMD
CF> > developers can have a look at it.
CF> >
CF> > hope that helps.
CF> >
CF> > cheers,
CF> > axel.
CF> >
CF> > CF>
CF> > CF> This suggests to me that there may be some issue with regard to the
CF> > number of
CF> > CF> atoms allowed? Is there a parameter I can change to account for this?
CF> > CF>
CF> > CF> Cheers
CF> > CF> Colin
CF> > CF>
CF> >
CF> > --
CF> > =======================================================================
CF> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
CF> > Center for Molecular Modeling -- University of Pennsylvania
CF> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
CF> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
CF> > =======================================================================
CF> > If you make something idiot-proof, the universe creates a better idiot.
CF> >
CF>
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
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.