Gromacs www.gromacs.org It is GPL. It can certainly handle metals, although as is always the case, you have to be careful in the choice of force field. It is fairly user friendly (by the standards of that field ;-). Not sure what the situation is for Macs but certainly runs well on Linux.
Alternatives: charmm, amber, namd, etc etc Your suggested project is perfectly reasonable, but don't expect it to be a day's work .... HTH Martyn On Thu, 2008-07-03 at 11:30 +0100, David Briggs wrote: > Hi everyone. > > I have a slightly off topic question I hope someone can help with. > > I have a structure of a wild type domain, which binds metal ions. > Certain mutations in chelating residues cause changes in the apparent > affinity for said metal ions. > > As I have (so far) failed to crystallise the mutant, I would like to > do some molecular dynamics in a water box, (with afore mentioned > mutations) to get a handle on the origin of the change in metal ion > affinity. > > Does anyone know of a suitable package which: > > a) is open source, or basically free to academics > b) allows inclusion of metal ions > c) gives an understandable and interpretable output, in terms of > changes in energy, etc. > d) Preferably runs on mac, (although I do have access to linux as well.) > > Am I asking for the moon on a stick? > > Looking forward to your responses. > > Regards, > > Dave -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: [EMAIL PROTECTED] * * Fax: +44 1925 603825 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
