Misleading failure of VMD with charge/CGenFF from waterbox

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Nov 23 2014 - 03:21:38 CST

I was successful in getting integer correct charge when generating both
nonsolvated, solvated, and neutralized psf/pdb in spite of long charmm36
atomtypes (CGenFF) for the ligand. That by adding "NAMD" at the first line
of psf file. Notice that neutralization was not necessary as the system was
already neutral.

When I wanted to set 0.15M NaCl, to make isotonic the system, by adding
"NAMD" to the solvated psf, the warning was "non integer charge" Actually,
this was a false message, as the correct number of CLA/SOD was added.
Adding "NAMD" to the final, isotonic psf file led in fact VMD to report
neutral system (without "NAMD" charge 57.59).

Irrelevant as this turns out to be, probably developers want to correct it
in a future version of VMD

francesco pietra

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