Hi,
Bond types (1, 2, 3, 6, 7, 8, 9) assigned by bondtype are needed to
correctly assign some atom types. See the atom type definition files in
$AMBERHOME/dat/antechamber for details
Best
Junmei
On Tue, May 19, 2009 at 10:50 AM, rebeca <rebeca.mmb.pcb.ub.es> wrote:
> Hello,
> 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
>
> Why are some bonds considered as "ar" and others considered as "2"? I have
> checked the bonds considered as "2" by the program and they are equivalent
> to the same ones considered as "ar" in the other ring. Would be any problem
> if I consider "ar" for all C-C bonds?
>
> Thank you very much in advance.
>
> Best wishes,
>
> Rebeca.
>
> --
> Rebeca García Fandiño
> Molecular Modelling and Bioinformatics Group
> Institut de Reçerca Biomèdica
> Parc Cientific de Barcelona
> 08028 Barcelona
> rebeca.mmb.pcb.ub.es
>
>
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Received on Fri May 22 2009 - 01:11:00 PDT
