This directory contains five files:

1. mkpsf_6waq.tcl -- VMD/psfgen script that creates the first vacuum psf/pdb pair. All NAG's are included.
2. my_6waq_vac.namd -- NAMD configuration file used to relax the "guessed" coordinates resulting from step 1.
3. my_6waq_solv.tcl -- VMD script that uses solvate and autoionize to generate a neutralized, solvated MD system using the coordinates from step 2 as input.
4. my_6waq_solv.namd -- NAMD configuration file that performs a minimization and short MD of the raw solvated system
5. my_6waq_solv_stageN.namd -- NAMD configuration file template for perform ing a minimization and series of short MD simulations of the raw solvated system. This file is used if the -stage flag is set, as described below, to run the final solvated MD simulation in stages to avoid patch-grid errors.

Make sure PSFGEN_BASEDIR resolves to the root directory of your local copy of this repository (mine is ${HOME}/research/psfgen). It is also assumed below that CHARMRUN resolves to your local charmrun executable and NAMD2 resolves to your local NAMD2 executable. For me, these are /home/cfa/namd/NAMD_2.13_Source/Linux-x86_64-g++/charmrun and /home/cfa/namd/NAMD_2.13_Source/Linux-x86_64-g++/namd2.

$ mkdir 6waq
$ cd 6waq
$ $PSFGEN_BASEDIR/scripts/do_test.sh -pdb 6waq [-stage] [-npe #] [-psfgen_args [-seed #] [-rbdonlyA] [-rbdonlyC] [-chainsAB] [-chainCD]]

The optional -stage flag, if present, instructs the script to perform the solvated MD simulations in stages to avoid patch-grid errors arising from box shrinkage during volume equilibration. The -npe flag allows the user to specify the number of processing cores to use in the solvated MD simulation; 8 is the default. The optional -psfgen_args flag passes subsequent arguments to the mkpsf script. The optional -seed flag allows the user the specify the seed for the random-number generator. The -rbdonlyA'' preserves only chain A (RBD), -rbdonlyB'' preserves only chain B (another RBD), -chainsAB'' only preserves chain A and B, and -chainsCD'' preserves only chains C and D.

2017-2020, Cameron F Abrams