From: Jan Saam (saam_at_ks.uiuc.edu)
Date: Wed Jan 02 2008 - 15:48:27 CST
Dear Carlos,
curently CHARMM charges cannot yet be determined using paratool. You
have to do it manually following the protocol described in the original
CHARMM papers:
MacKerell Jr., A. D., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J.
Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L.
Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T.
Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith,
R. Stote, J. Straub, M.Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M.
Karplus. 1998. All-hydrogen empirical potential for molecular modeling
and dynamics studies of proteins using the CHARMM22 force field. J.
Phys. Chem. B 102:3586-3616.
MacKerell Jr., A. D., J. Wiorkiewicz-Kuczera and M. Karplus 1995 An
All-Atom Empirical Energy Function for the Simulation of Nucleic Acids
J. Am. Chem, Soc. 117:11946-11975
Also read Alex MacKerell's Parameter development tutorial:
http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf
*
<http://www.psc.edu/general/software/packages/charmm/tutorial/mackerell/PARAM_00.pdf>*other
info can be found here:
http://mackerell.umaryland.edu/Empirical_FF_Dev.html
We are eventually going to add CHARMM charges support in Paratool, but
it's going to take a couple more months...
Jan
carlos alberto gueto tettay wrote:
> Hi NAMD's user:
>
> I'm Carlos Gueto from UdeC, Colombia.... I'm trying to parametrize a ligand to performe my NAMD MD.... I have already made two QM calculations like the paratool user guide said..... but it doesn't say almost nothing about how determine Charmm charges... CAN SOMEBODY HELP ME ? PLEASE... I WOULD LIKE IF YOU CAN EXPLAIN ME STEP BY STEP...
>
>
> I'll appreciate your help and time....
>
>
>
> Humbly,
>
>
>
> Carlos Alberto Gueto Tettay
> Grupo de Quimica Cuantica y Teorica
> Universidad de Cartagena
> Cartagena, Colombia
> _________________________________________________________________
> Discover the new Windows Vista
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-- **************************************** Jan Saam Theoretical and Computational Biophysics Group 3061 Beckman Institute University of Illinois 405 N. Mathews Ave Urbana, IL 61801 Phone: (217) 244-1928 Fax: (217) 244-6078 saam_at_ks.uiuc.edu
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