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 Wed May 20 2009 - 17:30:16 PDT
