From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Nov 20 2014 - 09:18:45 CST
Dear NAMD users,
I've noticed that the CHARMM force field distribution contains the
NBFIX parameters for Na+ ions and carboxylate oxygen atoms for
non-lipid systems:
SOD OC -0.07502 3.23 ! For prot carboxylate groups
SOD OC2D2 -0.07502 3.23 ! For carb carboxylate groups
SOD OG2D2 -0.07502 3.23 ! For CGenFF carboxylate groups
The paper (dx.doi.org/10.1021/jp401512z) in which these NBFIX
parameters were given was about lipids, but in the last line the
authors say:
"Likewise, the NBFIX values obtained here could be applied
to other biopolymers but also require validation. The
environment on a membrane surface differs from that of a
protein or DNA."
Are people using these NBFIXes for proteins? With CGenFF? Has the
validation mentioned in the paper been done by anyone? Are people just
assuming using the NBFIX is as good or better than not using it? I'm
inclined to do the latter.
Thanks,
Jeff
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