Dear Dian Jiao,
You should look at the output of the semi-empirical tool used
(divcon/mopac/sqm/...): It looks like the job failed... My
understanding is that a job performed with a semi-empirical method
should be fast (in particular, if the optimization threshold is loose).
You reported "pep.pdb": does it mean an entire peptide is involved in
the computation? in general, one wants to generate a new force field
library only for a modified residue; the regular residues are handled
by the Amber Force Filed Topology DataBase...
regards, Francois
> I was trying to model this peptide with the following command:
>
> antechamber -i pep.pdb -fi pdb -o pep.mol2 -fo mol2 -c bcc.
>
> After about 24 hours, the job "finished" except that it didn't generate
> pep.mol2 file. All other output files seem okay, including
> ANTECHAMBER_BOND_TYPE.AC0, ANTECHAMBER_AM1BCC_PRE.AC, sqm.in and sqm.out.
> So what happened to mol2? Was the file written to somewhere else?
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Received on Tue Jan 31 2012 - 00:30:03 PST
