VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jul 17 2013 - 12:48:36 CDT

In this connection I also wonder how molefacture treats pyrrole,
either quasi-aromatic or localized C=C, in order that the total charge
is zero.
Thanks
francesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Wed, Jul 17, 2013 at 5:14 PM
Subject: vmd-l: FFTK and CGenFF
To: vmd-l_at_ks.uiuc.edu

Hello:
I wonder whether CGenFF can be of any help to set up parameters for a
new ligand of a protein with FFTK for NAMD.

As there are atom types not comprised directly in CHARMM FF v 27, I
used CGenFF before going to MOLEFACTURE, however getting atom types
for CHARMM ff version 36.

I know there is a flag for NAMD to use CHARMM mode dealing with L-J,
however, has v27 been combined with v36? Can them be used for the same
run?

thanks
francesco pietra