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
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Received on Wed May 20 2009 - 17:30:23 PDT
