[AMBER] problem in running antechamber

From: Anshuman Dixit <anshumandixit.gmail.com>
Date: Tue, 26 Mar 2013 13:09:08 +0530

Dear Users,
I am trying to generate parameters for CIS-SYN CYCLOBUTANE THYMINE DIMER.
The pdb file with the structure is attached. The structure has a net charge
of -2.
I am running the following command:
antechamber -i TTD_f.pdb -fi pdb -o TTD_new.mol2 -fo mol2 -c bcc -nc -2 -m
2 -s 2

Running: /opt/apps/amber/amber12/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Info: Bond types are assigned for valence state 14 with penalty of 2

Running: /opt/apps/amber/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 317; net charge: -2
INFO: Number of electrons is odd: 317
      Please check the total charge (-nc flag) and spin multiplicity (-m
flag)

Running: /opt/apps/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/opt/apps/amber/amber12/bin/sqm -O -i sqm.in -o sqm.out"
of bcc() in charge.c properly, exit

Here is the output of sqm.out
 --------------------------------------------------------
                             AMBER SQM VERSION 12

                                     By
              Ross C. Walker, Michael F. Crowley, Scott Brozell,
                Tim Giese, Andreas W. Goetz and David A. Case

            --------------------------------------------------------


--------------------------------------------------------------------------------
  QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 221)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
calculation.

What should I do to correctly generate parameters using antechamber?

-- 
Dr. Anshuman Dixit
Scientist
Institute of Life Sciences
(An Autonomous Institute of Dept. of Biotechnology, Govt. of India)
Nalco Square, Chandrasekharpur, Bhubaneswar
India-751023



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Received on Tue Mar 26 2013 - 01:00:03 PDT
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