VMD-L Mailing List

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Mon Mar 25 2019 - 21:37:32 CDT

Dear VMD users,
I want to generate a molecule with a CL bond. And to get the topology
information, I have used the new version of the parmchk (which uses CGenFF
4.0). However, since the new version supports the lonepair for halogens, my
STR file has the following line
LONEPAIR COLI LP1 CL C2 DIST 1.6400 SCAL 0.0
However, when the psfgen reading the STR file, it throws the following
error,
psfgen) ERROR! FAILED TO RECOGNIZE LONEPAIR. Line 69: LONEPAIR COLI LP1
  CL C2 DIST 1.6400 SCAL 0.0
Does this mean VMD psfgen still does not support lonepair implementation
for NAMD input generation?. If that is so, what other ways can I
incorporate the lone pair related topology to the psf file?.

Best, 

-- 
Aravinda Munasinghe,