Just out of curiosity, and to help me configuring my own environment, what do people use besides Modeller in their modelling projects? I have an Intel/Linux box, 2 IBM workstations (AIX) and an Intel/MS-Win machine. My interest is in modelling peptides in the range of 40-120 amino acids, with high cysteine contents, homology with known structures usually below 50%. I would also like to do energy minimizations and molecular dynamics, and to analyse the MD trajectories.
Software that I am somewhat familiar with are: MSI-Accelrys InsightII Modeller VMD SPDBViewer (Deep View) Rasmol/Rastop Cn3D WebLabViewer Procheck Antheprot
Some additional software which I have access to but not much experience: gOpenMol ICMLite MolMol Whatif
What would you Modellers suggest as an ideal lab setup for homology modelling + MD + visualizations of structures and trajectories, considering the hardware above?
Ari M. Siqueira, PhD (a hopeful modeller...)