AMBER Archive (2005)

Subject: AMBER: PSC Summer Workshop: Modeling Proteins and Nucleic Acids with AMBER, VMD and the MMTSB Toolkit

From: Troy Wymore (wymore_at_psc.edu)
Date: Thu Feb 17 2005 - 13:00:36 CST

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PSC BIOMEDICAL INITIATIVE WORKSHOP 2005

        MODELING PROTEINS AND NUCLEIC ACIDS WITH AMBER,
        VMD AND THE MMTSB TOOLKIT

        Instructors: Professor David A. Case
                        Dr. Michael Crowley
                        Dr. Ross Walker

        June 9-12
        Application Deadline: April 25

This workshop is funded by grants from the NIH National Center for
Research Resources. These grants provide tuition, hotel, supercomputing
time, and workshop materials for US academic participants.

--------------------------
This workshop will cover the theory and practice of biomolecular
simulations using the Amber suite of programs. The lectures will cover
the use of molecular mechanics force fields, the theory of solvation
effects, and the connections between simulations and thermodyanmic
quantitites. Hands-on exercises will show how both implicit solvent and
explicit solvent simulations can be carried out, visualized, and
critically examined; participants are urged to bring specific projects
from their own labs to use as examples. More advanced topics will include
treating part of the system (such as an enzyme active site) as a quantum
region; using free energy simulations to estimate thermodynamic
quantities; and using the MMTSB toolkit to accelerate sampling and to
organize large-scale conformational explorations.

Participants should have an understanding of physical chemistry at the
undergraduate level, and be familiar with the basics of protein and/or
nucleic acid struture and chemistry. Basic familiarity with the UNIX or
Linux operating systems will be helpful. More information on the software
to be used can be found at http://amber.scripps.edu (Amber),
http://www.ks.uiuc.edu/Research/vmd (VMD), and http://mmtsb.scripps.edu
(MMTSB)

For specific details, including an electronic application form, see:

www.psc.edu/biomed/training/workshops/2005/Amber/index.html

If you have any questions, please contact Nancy Blankenstein at
blankens_at_psc.edu

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