AMBER Archive (2009)

Subject: Re: [AMBER] RESP using antechamber with Se atom

From: subarna thakur (thakur.subarna_at_yahoo.co.in)
Date: Thu Nov 05 2009 - 23:21:46 CST

Hi Donald
Are u able to optimize your structure using gaussian? Or  have you calculated the ESP charges based on single points? I am facing a silimar problem for Fe4s4 cluster and I have been told that antechamber cant be used for calculating RESP charges of transition metals like Fe.

Regards
Subarna
Ph.D student 
University of North Bengal
India

________________________________
From: Donald Keidel <dkeidel_at_scripps.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Fri, 6 November, 2009 12:51:37 AM
Subject: [AMBER] RESP using antechamber with Se atom

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

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