[AMBER] Side chain and backbone-specific parameters.

From: Lee-Ping Wang <leeping.stanford.edu>
Date: Tue, 10 Jun 2014 10:25:24 -0700

Hi everyone,


I'm working on some new protein force fields which have distinct backbone /
sidechain parameters for different amino acids. My parameterizations are
done using Gromacs, which allows atom-specific bonded interactions (i.e.
overriding the values that come from atom classes).


I don't see this functionality in AMBER, and it looks like the ff99sb-ildn
and ff12sb models have extra atom classes to accommodate the extra torsions.
Since I plan to port my force fields to AMBER, I'd like your advice on how
to do this most effectively.


What is the best way to implement residue-specific backbone and side chain
parameters? Should this be done by adding many atom classes? Is it even
possible to add on the order of 100 atom classes?




- Lee-Ping


AMBER mailing list
Received on Tue Jun 10 2014 - 10:30:03 PDT
Custom Search