Notes/Slides: (Acrobat PDF Files) Get Acrobat Reader Here!
Course Syllabus (PDF)
Assignments
Gromacs MDP File Templates: (Text Files)
Gromacs Automation Script
Dock Input Files:
Amber Input Files:
Useful Amber Perl Scripts:
Tutorials
(grouped by topic): (Acrobat PDF Files)
Sybyl Stuff
Sybyl Introduction (PDF)
Sybyl Biopolymer (PDF)
Docking:
UCSF DOCK Intro (PDF)
Autodock tutorials (Autodock web)
Molecular Dynamics:
AMBER Workshop (PDF)
oxyt.pdb (AMBER wkshp file)
AMBER Drug/DNA Workshop (PDF)
pet.pdb (drug structure file for AMBER Drug/DNA Workshop)
dna.pdb (equil DNA file for AMBER Drug/DNA Workshop)
autosan.perl (Amber automation script)
Study of Spider Toxin (Gromacs intro)
Drug-Enzyme complex (Gromacs)
trp_minv.pdb (GMX Drug_Enz)
amber94_nvt.svl (moebatch script file)
Amber Generalized Born Workshop
Amber GB tutorial (PDF)
Viewers, etc.
Molscript Tutorial (PDF)
GRASP Tutorial (PDF)
cef_pep.pdb file for Grasp tutorial
Patanol animation (mpeg file): Animation created using Gromacs and gOpenMol.
Delphi Workshop
Delphi tutorial (PDF)