On Fri, Apr 12, 2013 at 1:20 AM, parul sharma <sharmaparul7373.gmail.com>wrote:
> Dear Amber Users,
>
> I want to simulate a pharmaceutical compound and want to generate its crd
> and top files. In order to do so I used ANTECHAMBER to generate its mol2
> file calculate the charges and atom types. I used the following command.
>
> root.parul-desktop:/home/parul/Desktop/ns3 complex/org# antechamber -i
> org_h.pdb -fi pdb -o org_h.mol2 -fo mol2 -c bcc -s 2
>
> Running: /home/parul/amber12/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC<http://antechamber_bond_type.ac/> -f
> ac
>
> Running: /home/parul/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC <http://antechamber_ac.ac/> -p gaff
> Total number of electrons: 274; net charge: 0
>
> Running: /home/parul/amber12/bin/sqm -O -i sqm.in -o sqm.out
>
> Error: cannot run "/home/parul/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
> bcc() in charge.c properly, exit
>
> Also i believe it should have run the mopac.f, which i couldn't find in the
> bin directory.
>
No. Some time ago (at least 4 years, I think), we started using the sqm
program instead of mopac to run the semi-empirical QM calculations used to
derive bcc charges.
Look for the error in sqm.out to see what went wrong (and googling that
error message will help you solve the issue if it has been asked before).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 11 2013 - 23:30:02 PDT
