From: John Stone (
Date: Thu Dec 17 2020 - 22:54:15 CST

  Yes, to the degree possible, VMD tries to follow the PDB spec.
That said, there are many cases that exceed the PDB specification, e.g.,
such as when the system contains more than 99,999 atoms, and in
cases where various atom data field widths could exceed the legal
PDB spec.

When writing a trajectory frame to a PDB, one of the first issues is likely
to be the total atom count. Phenix is unlikely to handle things like
bulk water or other simulation components that don't typically occur
in crystallographic structures or cryo-EM derived model structures.

I don't know if Phenix expects the many hydrogens or other components to be
incorporated in the PDB, so thse are things worth checking and potentially
stripping out by using a VMD atom selection to remove parts of the
simulation that don't correspond to what would expect in a crystal structure.

Best regards,
  John Stone

On Fri, Dec 18, 2020 at 04:44:26AM +0000, Bennion, Brian wrote:
> The last time I checked, the VMD format for writing pdb files is exactly
> the standard as written on the pdb databank webpage.
> could you post the errors that phenix is having?
> --------------------------------------------------------------------------
> From: <> on behalf of
> McGuire, Kelly <>
> Sent: Thursday, December 17, 2020 4:52 PM
> To: VMD Mailing LIst <>
> Subject: vmd-l: PDB Format
> After running a long simulation and saving each frame of the trajectory as
> a PDB, we are trying to open those PDB files in Phenix and save them as
> MTZ files. However, Phenix does not like the PDB format that VMD
> creates. Phenix requires the same PDB format as that found from
> downloading a file from the protein data bank. An example of the required
> format we need can be given if requested. Does anyone have experience
> with Phenix and getting your PDB trajectory outputs into that program?
> Maybe another format that VMD does write may work?
> Dr. Kelly L. McGuire
> PhD Biophysics
> Department of Physiology and Developmental Biology
> Brigham Young University
> LSB 3050
> Provo, UT 84602

NIH Center for Macromolecular Modeling and Bioinformatics
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