apa@ccadfa.adfa.oz.au (Alan P Arnold) (10/24/90)
A query to bioinorganic molecular mechanikers and dynamikers out there: Here in Canberra, we are beginning to use Kollman's Amber 3.0 on a Convex C1XP to complement NMR studies of conformational changes induced in small bioactive peptides (<20mers) by metal-ions such as zinc and cadmium. However, the Convex version of Amber does not produce pretty pictures! At the moment, in order to visualise energy-minimised structures we send the Brookhaven Protein Database coordinate files produced by Amber down to my MacII running Chem3D+ (Cambridge Scientific). This is a *very* tedious process and fraught with problems, however the shaded space-filling movies that Chem3D+ produces are good (if you've got lots of RAM). As we are hopeful of obtaining an IBM RS6000 for this work in the near future, Iwould like to hear from users of molecular mechanics and dynamics packages, particularly Amber (but also Gromos) on these machines or the Convex. In particular, what programs do you use to visualise and rotate molecules, either statically or better, dynamically (movies)? Apart from extremely expensive (but undoubtely powerful) commercial packages (eg from Polygen), MIDAS and MacroModel come to mind, but I have no experience with these. (I have used Tripos' AlchemyII on a Compaq). As well as metal-ion complexes of biopeptides, we are also actively working on (synthesis, thermodynamics, kinetics, NMR) transition metal-ion complexes of multidentate ligands such as cryptands and cages. 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? ---- Alan Arnold | Phone: +61 62 68 8080 Chem. Department,University College | ACSNET: apa@ccadfa.oz Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV
troyer@cgl.ucsf.edu (John M. Troyer) (10/25/90)
In <1982@ccadfa.adfa.oz.au> apa@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@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@ccadfa.oz >Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb >CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV John Troyer troyer@cgl.ucsf.edu Dept. Pharmaceutical Chemistry troyer@ucsfcgl (bitnet) University of California ...!ucbvax!ucsfcgl!troyer San Francisco, CA 94117-0446