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 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