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GROMACS Introductory Tutorial - University of (GROMACS入门教程,大学)
GROMACS Tutorial
GROMACS Introductory Tutorial
Gromacs ver 3.3.1
Author: John E. Kerrigan, Ph.D.
AST/IST, University of Medicine and Dentistry of NJ
675 Hoes Lane
Piscataway, NJ 08554
Phone: (732) 235-4473
Fax: (732) 235-5252
Email: kerrigje@
1
GROMACS Tutorial
GROMACS Tutorial for Solvation Study of Spider Toxin Peptide.
Yu, H., Rosen, M. K., Saccomano, N. A., Phillips, D., Volkmann, R. A., Schreiber, S. L.:
Sequential assignment and structure determination of spider toxin omega-Aga-IVB.
Biochemistry 32 pp. 13123 (1993)
GROMACS is a high-end, high performance research tool designed for the study of protein
dynamics using classical molecular dynamics theory. [1] This versatile software package is Gnu
public license free software. You may download it from . GROMACS
runs on linux, unix, and on Windows (a recent development).
Synopsis. In this tutorial, you will study a toxin isolated from the venom of the funnel web spider.
Venom toxins have been used in the past to identify cation channels. Calcium ion channels regulate
the entry of this ion into cells. Nerve signals are highly governed by the balance of ions in neuronal
cells. It is hypothesized that exposed positively charged residues in venoms like the spider toxin
here bind favorably to the negatively charged entrance of the cell’s ion channel. The spider toxin in
this tutorial has its positively charged residues pointing predominantly to one side of the peptide.
The ion channel is blocked, resulting in blocked nerve signal leading to paralysis and ultimately to
death (presumably via respiratory failure).
We will study this peptide toxin using explicit solvation dynamics. First, we will compare an in
vacuo model to a solvated mod
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