Preparation of Input Files

 

All of the files used to prepare the PHE and TRP topology and coordinate files can be downloaded from here. Download the “dynamics.tar.bz2” file and unpack it using the command;

tar -jxvf dynamics.tar.bz2

This will result in a directory called “dynamics” that contains one directory each for PHE and TRP.


Inside each directory for the side-chains are a “parameterise”, “minimise” and “equilibrate” directory. These contain the files for generating the parameters for the side-chain and solvating it in a water box, minimising the side-chain in the water box, and equilibrating the side-chain in the water box using 1 nanosecond of molecular dynamics.


dynamics/SIDECHAIN/parameterise

This directory contains the files to generate the GAFF parameters for the side-chain and to solvate it in a box of TIP3P water. To start, a PDB of the side-chain was downloaded from the zinc database. This file (called SIDECHAIN.pdb) was processed using Antechamber (from AmberTools) using the commands in “create_params.cmd”. These generated AM1/BCC charges for the side-chain and added LJ and bond/angle/dihedral parameters from the GAFF forcefield. Next, the leap program (also from AmberTools) was used to solvate the side-chain in a water box that extended at least 15 angstroms from the side-chain. The file “leap.in” was used to configure leap, while the file “solvate.cmd” contains the command used to run leap. The result of this were the files SIDECHAIN_water.top and SIDECHAIN_water.crd which contain the parameterised side-chain in the water box.


dynamics/SIDECHAIN/minimise

This directory contains the files used to minimise the side-chain in the water box. The SIDECHAIN_water.top file from the parameterise directory was copied to dynamics/SIDECHAIN/SIDECHAIN.top. The SIDECHAIN_water.crd file from the parameterise directory was copied to this directory, and renamed SIDECHAIN.crd. This was used as the starting point for two rounds of minimisation, performed using the sander program that comes with Amber. Round 1 of minimisation was controlled using the command file “min1.in”, while round 2 was controlled using the command file “min2.in”. The commands used to perform minimisation are in “minimise.cmd”. The result is a file, min2_SIDECHAIN.crd, that contains the coordinates of the minimised side-chain in the minimised water box.


dynamics/SIDECHAIN/equilibrate

This directory contains the files used to equilibrate the side-chain in the water box. Equilibration was performed using the GPU-accelerated pmemd.CUDA program that comes with Amber. Equilibration involved three stages;


  1. (1)Heating from 0 to 298 K at constant volume for 100 picoseconds, controlled using the command file md1.in

  2. (2)Equilibration at 298 K at constant volume and temperature for 100 picoseconds, controlled using the command file md2.in

  3. (3)Equilibration at 298 K and 1 atmosphere pressure at constant pressure and temperature for 800 picoseconds, controlled using the command file md3.in


The min2_SIDECHAIN.crd file from the minimise directory was used as the input for stage 1, while stage 2 started from the output of stage 1, and stage 3 started from the output of stage 3. Equilibration was performed using the commands in the file “equilibrate.cmd”. You can visualise the trajectory by loading the “md1.traj”, “md2.traj” and “md3.traj” files into VMD (Amber coordinates with periodic box). The coordinates at the end of equilibration are held in md3.crd. This, together with the SIDECHAIN.top file were copied to SIDECHAIN.top and SIDECHAIN.crd as input for the QM/MM calculations in the workshop. To get the PDB file, the ambpdb program that comes with AmberTools was used, via the command;

$AMBERHOME/bin/ambpdb -p SIDECHAIN.top < SIDECHAIN.crd > SIDECHAIN.pdb