VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jul 18 2013 - 01:54:35 CDT

Hi Christopher:
Thanks a lot for commenting on molefacture/CGenFF/FFTK. I got confused
as I submitted a Sybyl mol2 file instead of a pdb file to molefacture.
Now, with a pdb file, no problem. I used a gamess us abinitio
minimized pdb file. Hope that that will speed up the FFTK procedure.

A question remains open (therefore I started a new thread with
appropriate title), i.e., whether, with namd (and psfgen), charmm36 ff
can be used for the organic ligand simultaneously with charmm27 ff for
the protein. As far as I can understand from namd manual, setting in
the flag vdwForceSwitching results in referring to charmm36 only. But
I may well have misinterpreted the manual.

Thanks

francesco pietra