Molecular Mechanics/Dynamics of Metal Complexes on IBM RS6000/Convex

John M. Troyer troyer at cgl.ucsf.edu
Thu Oct 25 11:54:30 EST 1990

In <1982 at ccadfa.adfa.oz.au> apa at ccadfa.adfa.oz.au (Alan P Arnold) writes:
>I would like to hear from users of molecular mechanics and dynamics packages, 
>In particular, what programs do you use to visualise and rotate molecules, 
>either statically or better, dynamically (movies)? 

I give this reference to everyone who asks this question:
	"Molecular modeling software and methods for medicinal 
	chemistry" Cohen NC, Blaney JM, Humblet C, Gund P, Barry DC
	Journal of Medicinal Chemistry 33:883-894, 1990.

This is a recent, good overview of molecular modeling and molecular graphics
packages, both commercial and academic. In order to do molecular graphics,
you will need a workstation. Anything else is (as you say) exceptionally
tedious. Here we use exclusively irises (and the program MIDAS, which was 
developed here.) 

As for looking at dynamics movies, there are several commerical packages
(referenced in the above article). For AMBER, Terry Lybrand has developed
a movie program for analysis of trajectories. I _think_ it's been deposited
in the QCPE, but I could dig up his address for anyone who's interested.

>I would also like to model 
>the mechanics and dynamics of these complexes using Amber/Gromos.  Does anyone 
>have a feel for how these packages (or the ones that you use) cope with 
>metal-ion force fields, particularly tertrahedral/octahedral geometries?

The answer: Not Well. You can fake it with constraints, but I don't know
of any good parameters out there. Dave Ferguson (ferguson at cgl.ucsf.edu)
has added the code to MM2 to deal with metals correctly. His program 
MM2MX is described in a paper in this month's J. Comput. Chem. 
Something similar may be added to AMBER in the future. You might want
to contact Ken Merz at Penn State. I gather he is currently writing a 
review on simulations with metals.

Hope this helps,

>Alan Arnold             	     |  Phone: +61 62 68 8080
>Chem. Department,University College  | ACSNET: apa at ccadfa.oz 
>Australian Defence Force Academy     |   UUCP: ...!seismo!munnari!ccadfa.oz!lpb 
>CANBERRA  ACT 2600 Australia         |   ARPA: apa%ccadfa.oz at SEISMO.CSS.GOV

John Troyer				troyer at cgl.ucsf.edu
Dept. Pharmaceutical Chemistry		troyer at ucsfcgl (bitnet)
University of California		...!ucbvax!ucsfcgl!troyer
San Francisco, CA 94117-0446

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