2016 AMBER tutorial with Beta Trypsin

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).

I. Introduction

Yaping

II. Structural Preparation

Antechamber, Parmchk, tLeap

Omar, Katie

III. Simulation using pmemd

PMEMD

Agatha, Beilei Making a new file called 01md.in:

mkdir 01md.in
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

ptraj.strip.wat.in:

trajin ../003.PMEMD/10md.trj 1 1000 1
trajin ../003.PMEMD/11md.trj 1 1000 1
trajout 1BJU.trj.strip nobox
strip :WAT

ptraj.rec.rmsd.in:

trajin 1BJU.trj.strip
trajout 1BJU.com.trj.stripfit 
reference ../002.ANTE.TLEAP/1BJU.com.gas.leap.rst7
rms reference out 1BJU.rmsd.CA.dat :1-223@CA

ptraj.lig.rmsd.in:

trajin 1BJU.com.trj.stripfit
reference ../002.ANTE.TLEAP/1BJU.com.gas.leap.rst7
rms reference out 1BJU.lig.rmsd.dat :224@C*,N*,O*,S* nofit

ptraj.strip.rec.in:

trajin 1BJU.com.trj.stripfit 1 2000 1
trajout 1BJU.lig.trj.stripfit
strip :1-223

ptraj.strip.lig.in:

trajin 1BJU.com.trj.stripfit 1 2000 1
trajout 1BJU.rec.trj.stripfit
strip :224

ptraj.dist.in:

trajin 1BJU.com.trj.stripfit
distance 171OD2_224N1 :171@OD2 :224@N1 out 171OD2_224N1.dat
distance 171OD1_224N2 :171@OD1 :224@N2 out 171OD1_224N2.dat

MM-GBSA Energy Calculation

Monaf