AMBER Archive (2009)

Subject: Re: [AMBER] gaff and aromatic compounds

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue May 19 2009 - 11:07:29 CDT

On Tue, May 19, 2009, rebeca wrote:

> I have a doubt about the parametrization of aromatic systems with the Gaff
> force field.
> For example, in the case of naphthalene, after
>
> $AMBERHOME/exe/antechamber -i naphthalene.pdb -fi pdb -o naphthalene.mol2
> -fo mol2 -c bcc -s 2 &
>
> the naphthalene.mol2 bond section is this one:
>
> @<TRIPOS>BOND
> 1 1 2 ar
> 2 1 3 ar
> 3 1 4 2
> 4 2 5 ar
> 5 2 6 2
> 6 3 8 ar
> 7 3 17 1
> 8 4 9 ar
> 9 4 16 1
> 10 5 7 ar
> 11 5 15 1
> 12 6 10 ar
> 13 6 14 1
> 14 7 8 ar
> 15 7 13 1
> 16 8 12 1
> 17 9 10 ar
> 18 9 11 1
> 19 10 18 1

The bond type is not directly used by Amber or gaff. What you need to check
is what the atom types are for various atoms, and what the actual bond force
constants and equilibrium angles are.

(cc-ing to Junmei, in case he sees something to fix here.)

...dac

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber