Re: charmm charge style

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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