VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Fri Oct 30 2020 - 07:17:00 CDT

Dear VMD users,

The new Molefacture 2.0 VMD plugin available at least from VMD version
1.9.4a38 is a surprise for me. I used Molefacture previously to prepare
PDB and PSF files for parametrization with FFTK. However, the new
version is missing the functionality which is necessary for this
purpose. Specifically, I am unable to edit:

  * atom names
  * atom types
  * partial charges (to set constant 0.09 charge on HA hydrogens)

Am I missing something? When I select a row in the table of atoms and
hover the pointer, say, over the atom type, I see the pointer changing
to a pen icon. It would suggest the ability to edit but I tried clicking
all buttons and typing, nothing works. Tried on Linux.

Could anyone suggest workarounds, or another tool able to start with a
simple PDB file? I know I can manualy edit the PDB file, prepare the
matching topology file and then use either autopsf or psfgen, but this
workflow  is more elaborate and error prone, and I need it for classes.

With regards,

Pawel