Principles of Drug Design

Benzamidine(BZA)-Trypsin Complex from Autodock 3 Docking.

Principles of Drug Design Course Files:

Autodock Tools Tutorial (Download Autodock Tools from here)

hcp_1bru.pdb

ita_1bio.pdb

pbn_1utp.pdb

pea_1uto.pdb

cza_1esb.pdb (Use the peptide aldehyde given here)

abn.pdb (Benzylamine)

apa.pdb (Aminophenylpyruvate)

apa.mol2

trp.pdb (Trypsin)

step1.awk

step2.awk (You will need to modify this file to reflect your pulling direction!)

prep.pdf (Instructions for installing NAMD/VMD et al. on your PC)

spartan_chg.pdf (How to use PC Spartan for computing partial atomic charges)

Useful Links:

psfgen users guide

CHARMM parameter and topology sets for NAMD

Cornell (Amber) paramter and topology sets for NAMD