From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Dec 11 2015 - 05:07:03 CST

Hello:

With CHARMM36, VMD in text mode, the .gen file including:

patch GLUP PRA:235
patch ASPP PRA:516

regenerate angles dihedrals

(the protein pdb included all H-atoms), the log file reports that it was
unable to read HE2 and HD2 for the above residues. The result was that
these atoms were put outside the protein.

On removing HE2 and HD2 from the pdb, no more such warnings, however,
again, both atoms placed outside the protein. Apparently the patch was
accepted.
..............................

Moreover, despite the error reported in the log file;

psfgen) Toplogy and parameter information for water and ions.
psfgen)
psfgen) ERROR! FAILED TO RECOGNIZE SET
psfgen) ERROR! FAILED TO RECOGNIZE SET
psfgen) ERROR! FAILED TO RECOGNIZE IF
psfgen) ERROR! FAILED TO RECOGNIZE READ
psfgen) Topology for water and ions
psfgen)
psfgen) ERROR! FAILED TO RECOGNIZE 31
psfgen) skipping statements at end of file due to end or return statement

a ligand CLA of the protein was set correctly. is there any possible
modification of the str file, or should I extract from it the relevant
portions in order to skip what VMD is unable to read from CHARMM36?
.....................................

Grateful for advice

francesco pietra