AMBER Archive (2009)

Subject: [AMBER] RESP using antechamber with Se atom

From: Donald Keidel (dkeidel_at_scripps.edu)
Date: Thu Nov 05 2009 - 13:21:37 CST

Hi,

I have calculated the electrostatic potential using gaussian 03 for
SELENOMETHIONINE. When calculating the esp I added to the gaussian
input file the vdw radius of Se. Gaussian terminated normally and there
is charge values in the gaussian output for Se.

when I run the following command:

antechamber -fi gout -fo ac -i input_MSE.gout -o input_MSE.ac -c resp

I get the folloowing output:

For atom[7]:Se1, the best APS is not zero, bonds involved by this atom
are frozen

The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
(aromatic double)Error: cannot run "/usr/local/amber10/bin/bondtype -j
full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit

I have searched the amber mail archive and found emails regarding Fe
with a similar error, but could not determine how to resolve this.

Is there a way for antechamber to recognize or find the Se information
in the gaussian output.

Thank you in advance for your help.

Don 

-- 
"The major difference between a thing that might go wrong and a thing that cannot possibly go wrong is that when a thing that cannot possibly go wrong goes wrong it usually turns out to be impossible to get at or repair."
  -- One of the laws of computers and programming revealed

                                      Douglas Adams in "Mostly Harmless"

_______________________________________________________________________

Donald J. Keidel, Ph.D.
Research Associate
The Scripps Research Institute
3377 N. Torrey Pines Court, Suite 100
La Jolla, CA 92037
mail code: TPC-26
phone:  (858) 784-2842
fax:  (858) 784-2341
dkeidel_at_scripps.edu
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber