AMBER Archive (2009)

Subject: [AMBER] gaff and aromatic compounds

From: rebeca (rebeca_at_mmb.pcb.ub.es)
Date: Tue May 19 2009 - 10:50:02 CDT


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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