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You can borrow some parameters from our following study on the p53 DNA binding domain: Molecular Dynamics Simulations of p53 DNA-Binding Domain, Lu, Q.; Tan, Y.-H.; Luo, R., J. Phys. Chem. B., 2007, 111(39), 11538-11545. In general, you'll have to do some QM calculations to get the parameters for your specific system. Best, Ray ========================================== Ray Luo, Ph.D. Dept Molecular Biology & Biochemistry University of California, Irvine, CA 92697 USPS: PO Box 3900 Phone: (949) 824-9528 Email: rluo.uci.edu Web: http://rayl0.bio.uci.edu/ ========================================== -----Original Message----- From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of Mattia Mori - CERM Sent: Wednesday, November 21, 2007 8:54 AM To: amber.scripps.edu Subject: AMBER: Zinc-Histidine force field Dear amber users, I'm trying to work with zinc protein but I got some problems during the parametrization with tleap. When I bound the Zn ion to the NE2 of the three histidins with the command "bond" and saveamberparm I get this error message: Could not find bond parameters for : NB - Zn Could not find angle parameters for: CV - NB - ZN Could not find angle parameters for: CR - NB - ZN ...... parameter files was not saved I think I've to built the .prep file and/or to modify the force field for my protein but I don't know how to do that. Do someone can tell me if there are some tutorials about? or where to find a reliable forcefield fo MMPs protein? thank you very much. Mattia
-- **-**-**-**-**-**-**-**-**-**-**-**-** Mattia Mori, PhD Student CERM - Centro di Risonanze Magnetiche via L. Sacconi 6,, 50019 Sesto Fiorentino, FI fax (+39) 055 4573914 tel (+39) 055 4573912 www.cerm.unifi.it----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu Received on Sun Nov 25 2007 - 06:07:18 PST