AMBER Archive (2009)

Subject: Re: [AMBER] gaff and aromatic compounds

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Fri May 22 2009 - 04:04:45 CDT

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_at_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_at_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_at_mmb.pcb.ub.es
>>
>>
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>>
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-- 
Rebeca García Fandiño
Molecular Modelling and Bioinformatics Group
Institut de Reçerca Biomèdica 
Parc Cientific de Barcelona
08028 Barcelona
rebeca_at_mmb.pcb.ub.es

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