Re: [AMBER] RESP using antechamber with Se atom

From: subarna thakur <thakur.subarna.yahoo.co.in>
Date: Fri, 6 Nov 2009 10:51:46 +0530 (IST)

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.scripps.edu> To: AMBER Mailing List <amber.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.scripps.edu webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Connect more, do more and share more with Yahoo! India Mail. Learn more. http://in.overview.mail.yahoo.com/
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Received on Thu Nov 05 2009 - 21:30:02 PST
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