In antechamber, we use seven bond types (1, 2, 3, 6, 7, 8, 9). 7 is aromatic
single and 8 is aromatic double. However in some format, such as mol2, there
are fewer bond types and both 7 and 8 belong to "ar". Therefore, you will
some "discrepancy" between different formats.
Best
Junmei
On Fri, May 22, 2009 at 4:04 AM, rebeca <rebeca.mmb.pcb.ub.es> wrote:
> Hi,
> thank you very much for your answer, however I don´t understand why in
> some cases the bond is assigned as "ar" and the equivalent bond is assigned
> as "2". Would it be a correct deffinition for naphtalene?
>
>
> On Thu, 21 May 2009 20:24:52 -0500, Junmei Wang <junmwang.gmail.com>
> wrote:
> > 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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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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 Wed May 27 2009 - 01:10:52 PDT
