Difference between revisions of "2016 AMBER tutorial with Beta Trypsin"
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Agatha, Beilei | Agatha, Beilei | ||
| + | 01mi.in: equilibration | ||
| + | &cntrl | ||
| + | imin = 1, maxcyc = 1000, ntmin = 2, | ||
| + | ntx = 1, ntc = 1, ntf = 1, | ||
| + | ntb = 1, ntp = 0, | ||
| + | ntwx = 1000, ntwe = 0, ntpr = 1000, | ||
| + | cut = 8.0, | ||
| + | ntr = 1, | ||
| + | restraintmask = ':1-224 & !@H=', | ||
| + | restraint_wt = 5.0, | ||
| + | / | ||
==IV. Simulation Analysis== | ==IV. Simulation Analysis== | ||
Revision as of 14:53, 6 April 2016
For additional Rizzo Lab tutorials see AMBER Tutorials.
In this tutorial, we will learn how to run a molecular dynamics simulation of a protein-ligand complex. We will then post-process that simulation by calculating structural fluctuations (with RMSD) and free energies of binding (MM-GBSA).
Contents
I. Introduction
Yaping
II. Structural Preparation
Antechamber, Parmchk, tLeap
Omar, Katie
III. Simulation using pmemd
PMEMD
Agatha, Beilei
01mi.in: equilibration &cntrl imin = 1, maxcyc = 1000, ntmin = 2, ntx = 1, ntc = 1, ntf = 1, ntb = 1, ntp = 0, ntwx = 1000, ntwe = 0, ntpr = 1000, cut = 8.0, ntr = 1, restraintmask = ':1-224 & !@H=', restraint_wt = 5.0,
/
IV. Simulation Analysis
Ptraj
Lauren, Haoyue
MM-GBSA Energy Calculation
Monaf
