From: Axel Kohlmeyer (
Date: Thu Jan 04 2007 - 11:46:39 CST

On Thu, 4 Jan 2007, Per Jr. Greisen wrote:

PG> Hey,
PG> I have a MD simulation and I want to save a structure from the simulation.
PG> So I use the function "Save coordinates..." in VMD and save the structure
PG> I would like but in the generated pdb file there has been added a bond
PG> between to hydrogens on NAD+ which should not be there. Also if I try to


please note, that VMD generated .pdb file contain no bond information.
the bond information is generated heuristically upon reading the
coordinates. if you'd also save a .psf file, VMD would recognize
the bonding information stored there. note, that this .psf file
cannot be used for simulations only for visualization, as it only
contains a subset of the information needed (e.g. no angles/dihedrals).

PG> color type nothing changes from color by name. How to fix this problem?

please explain what you'd expect. most likely this is again due to
lost information by writing the .pdb file.


PG> (I have added the NAD+ structure)
PG> Thanks in advance

Axel Kohlmeyer
   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.