Dear Amber users,
I have a question about generating electrostatic potential maps for
snapshots of a trajectory. I've read that it's possible to us PBSA within
AMBER, but this sounds like one would have to use an mdin file to computer
different snapshots. This sounds like a time-intensive method that also
needs to use AMBER itself; I'm wondering if there is a way I can use
AmberTools or any other program on my personal computer. I'm also not sure
if it's appropriate to use PBSA with the explicit-solvent simulations that
I want to analyze.
I've been looking into the APBS software (
http://www.poissonboltzmann.org/apbs) for which VMD has a plugin, but that
requires loading of a parm file, and since I use parmbsc0+chiOL3 as well as
a different parm file for a noncanonical base pair, I'm not sure of a
simple way to load the force field that I'm using.
I realize this is a broad question, so any insight that anyone can provide
would be greatly appreciated!
Thank you all,
Kamali Sripathi
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Received on Sat Jan 26 2013 - 07:30:02 PST
