(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

AMBER Advanced Tutorial 25
SECTION 2

GIST Analysis Example
Analysis of water thermodynamics using Grid Inhomogeneous Solvation Theory of Factor Xa active site.

By Romelia Salomon, Crystal Nguyen, Steven Ramsey, Jonathan D. Gough, Mike Gilson, Tom Kurtzman, & Ross Walker

2) Running the MD calculations to collect frames for GIST

Now that we have relaxed our structure, prod_100ns.rst7, we need to run a long MD simulation inorder to collect the necessary frames to run our analysis with GIST.

For this tutorial, we have run a 100 ns long MD production simulation. Due to space limitations, we have not included the full trajectory, and only present the results of the GIST analysis. To reproduce the results in this paper one would need to run this simulation to generate your own trajectory file.

md-nvt-100ns.in
Production run 100ns nvt
 &cntrl
  imin=0,
  ntpr   = 500,    ntwx   = 500,
  ntwr   = -500000,
  iwrap=1,
  ntx=5, irest=1,
  ntf    = 2,       ntb    = 1,
  ntc    = 2,       cut    = 9.0,
  nstlim = 50000000,
  dt     = 0.002,
  nscm   = 1000,
  temp0  = 300.0,
  ntt    = 3, gamma_ln = 2.0,
  ntr=1, restraint_wt=100,
  restraintmask=':1-234',
  ig=-1,
 &end


  

We can now run this using pmemd. For example, to run using 2 processors on a dual cpu desktop:

mpirun -np 2 $AMBERHOME/bin/pmemd.MPI -O -i md-nvt-100ns.in -o md-nvt-100ns.out -p ChA_IONS_disul_TIP3P.prmtop -c prod_100ns.rst7 -r final-prod.rst7 -x prod_100ns.nc -ref prod_100ns.rst7

The original trajectory file produced is significantly large, about 33GB, so we have not included it here. You can use the files provided to run the calculation. As stated before, this will generate a statistically equivalent trajectory. Our 100ns trajectory, on a single GPU GeForce GTX 690, took ~52 hrs

IMPORTANT: Note that an MD trajectory for GIST analysis should be performed with the solute (e.g. the protein) restrained, as shown in the previous input file. Failure to do so will cause the GIST analysis to have a lot of noise. If the solute is rigid, one can run without restraints and then post-process the trajectory such that the solute is aligned across all frames.

A basic cpptraj script (image.ptraj) can be used to allign the trajectory to a reference frame.

In this example the trajectory is referenced to all heavy atoms of the initial frame

parm ChA_IONS_disul_TIP3P.prmtop
trajin prod_100.ns.nc
reference ChA_IONS_disul_TIP3P.inpcrd
center reference ':1-234 & !@H'
autoimage
trajout prod_100ns_aligned.nc
go
quit

To run this script:

cpptraj -i image.ptraj > image.ptraj.out &

To this point we have shown how to generate a series of frames to be analyzed using GIST. We can now proceed to Section 3 where we will use GIST to analyze the hydration of the binding pocket of Factor Xa.


CLICK HERE TO GO TO SECTION 3


(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015