Dear Amber uses,
I'm trying to use GAFF to describe the interaction in a polymer system. I
have parameter data files of GAFF and already read them several times. Now I
have some questions on this force field.
The first one is about atomic charges. I couldn't find the charge value for
any given atom. It seems to me that the charge value is obtained by running
some tool in Amber software package. Is it right? Does anyone know other
ways to obtain atomic charges for a simple polymer (let's say, the repeat
units in a polymer chain only include three types of atoms: C3,C2 and hc,
only have five types of bonds: C3-C3,C2-C2,C3-C2,HC-C3,HC-C2) without using
any Amber tools?
The second one is about the total number of dihedrals. Is it necessary to
use the torsion potential of GAFF for all the dihedrals? For instance, for a
chemical structure like CH3-CH=CH-CH3, do I need to take care of all the
dihedrals (the total number: 12): C3-C2-C2-C3, Hc(1)-C3-C2-C2,
Hc(2)-C3-C2-C2, Hc(3)-C3-C2-C2, Hc(1)-C3-C2-Hc,Hc(2)-C3-C2-Hc,
Hc(3)-C3-C2-Hc,Hc-C2=C2-C3,Hc-C2=C2-Hc,Hc-C2-C3-Hc(1), Hc-C2-C3-Hc(2),
Hc-C2-C3-Hc(3)? If so, I could find the parameter values for X-C3-C3-X,
X-C2-C2-X, X-C3-C2-X, HC-C3-C2-C2, but I could not find the parameter values
for Hc-C3-C3-Hc, Hc-C2-C2-HC, Hc-C2-C2-C3, Hc-C3-C2-Hc? Then, do it means, I
have to use the same values in the generalized forms: X-C3-C3-X, X-C2-C2-X,
X-C3-C2-X for the dihedrals with carbon-hydrogen bonds?
Does anyone use the GAFF for some polymer systems? Your any suggestions or
experience will be highly appreciated.
Lan
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Received on Fri Sep 02 2011 - 13:00:03 PDT
