how to setup a nice modelling environment?

["Ari M. Siqueira" <siqueira AT icb.ufmg.br>]

Hi,

 

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?

 

Please advise.

 

Yours thankfully,

 

Ari M. Siqueira, PhD

(a hopeful modeller...)