Re: [AMBER] problem in running antechamber

From: M. L. Dodson <>
Date: Tue, 26 Mar 2013 04:22:14 -0500

On Mar 26, 2013, at 2:39 AM, Anshuman Dixit wrote:

> 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
> 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
> 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 -o sqm.out
> Error: cannot run "/opt/apps/amber/amber12/bin/sqm -O -i -o sqm.out"
> of bcc() in charge.c properly, exit
> Here is the output of sqm.out
> --------------------------------------------------------
> By
> Ross C. Walker, Michael F. Crowley, Scott Brozell,
> Tim Giese, Andreas W. Goetz and David A. Case
> --------------------------------------------------------
> --------------------------------------------------------------------------------
> --------------------------------------------------------------------------------
> 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?

The structure in the pdb file is not that of a closed shell electronic compound,
a necessary condition for using antechamber and the associated utility programs.
At a minimum, the 5'-phosphate should have an -OH added. I suggest that more
realistic capping structures would be -O-methyl at each end. I also suggest
that this is a sufficiently difficult problem that it would be useful to
establish a collaboration with or seek the guidance of Dr. F.-Y. Dupradeau via
the RED email list forum. Information is available at

In my opinion, RED would be a better tool than antechamber to develop the
partial atomic charges necessary for this DNA residue descriptor. Information
and descriptions at the web site led me to this
conclusion, and I recommend the site to you. Dr. Dupradeau is an expert in RED
and in using appropriate capping structures to generate force field residue
definitions that use RESP charges.

I seriously considered doing exactly this project before I retired several years
ago. If I had continued, I would have tried to enter into a collaboration with
Dr. Dupradeau. At a minimum I would have sought his guidance. From reading his
postings on both the AMBER and q4md-forcefieldtools email lists, he also seems
to be very open to helping others use the RED tools.

Bud Dodson
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Tue Mar 26 2013 - 02:30:02 PDT
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