On Sun, May 19, 2013 at 2:07 PM, Cenk (Jenk) Andac <cenk_andac.yahoo.com>wrote:
> Dear Amber users,
>
> I am currently working on AM1-BCC charge computation by the antechamber
> module of amber.
> I seem to have a problem with charge computation.
>
> My molecule has a zero charge.
>
> here is the antechamber chamber command I use
>
> antechamber -s 2 -i t1.mol2 -fi mol -o mol.mol2 -fo mol2 -at gaff -c bcc
> -nc 0 -m 1 -rn MOL -j 4
>
-fi should be "mol2", not "mol", I think.
>
> Running: /usr/local/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Total number of electrons: 0; net charge: 0
>
Your system has 0 electrons. Coupled with a net charge of 0, this is
impossible for anything except a vacuum ;). What this indicates to me is
that the input file was improperly parsed, yet the parser did not choke on
any particular line of the input file so there was no helpful error message
to that effect.
It could be that antechamber did not know how to interpret a "mol" file
(which does not appear to be supported according to the output of
"antechamber -L". If you're still getting the same error after
substituting mol2 for mol as I suggested above, then I suggest trying to go
through a PDB file first. PDB (or gaussian output) tends to be more common
input to antechamber. There are numerous tools that will convert from mol2
to PDB (e.g., OpenBabel).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun May 19 2013 - 12:30:03 PDT
