VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Dec 17 2020 - 22:44:26 CST

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: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Thursday, December 17, 2020 4:52 PM
To: VMD Mailing LIst <vmd-l_at_ks.uiuc.edu>
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