VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Dec 19 2018 - 18:46:23 CST

Hi all,

A new student caused an issue that I hadn’t seen before. She loaded a PDB and then a PSF and then wrote a PSF. However, the atom types were all initialized to the atom names (by the PDB reader) and then weren’t overwritten by the PSF reader. It seems to me like you would always want to take the atom types from a PSF if you read it in, no matter what was loaded before?

It seems to come down to the optflags in the molfile plugins. However, there isn’t a MOLFILE_TYPE or MOLFILE_ATOMTYPE flag, so maybe it would be more complicated than a one line fix in psfplugin.c? It’s not a big deal, so I only bring it up if others agree it’s not currently the expected behavior and it’s easy to fix.

Thanks!
JC