rDock is a fast & free docking program designed to be used in High-Throughput Virtual Screening. This is a summary of the steps necessary to do so. You must have previously defined yor system & cavity (consult the manual)

PART 1: DEFINING THE RIGHT PARAMETERS FOR HT-MODE

Start by executing 50 docking runs for a set of ligands representative og your entire collection:

rbdock -i $f -o ${f}_out -r REC.prm -p dock.prm -n 50 > ${f}_out}.log

rDock is a fast & free docking program designed to be used in High-Throughput Virtual Screening. This is a summary of the steps necessary to do so.

1) You mst have previously defined yor system & cavity (consult the manual)

2) Execute 50 docking runs for a set of ligands representative og your entire collection:

rbdock -i $f -o ${f}_out -r REC.prm -p dock.prm -n 50 > ${f}_out}.log

So, your output files are named *_out.sd. Create a report file:

amber2namd.pl

Have run a simulation with AMBER and want to continue with NAMD? That's what you need:

Usage:

perl amber2namd.pl amber_topology_file amber_restart_file root_namd_files

It creates a NAMD configuration file with all the needed periodic boundary definitions (assumes for truncated octahedron) + a velocities PDB file (needs ambpdb) to do a proper restart.

Note that:

1) there may be some difference in the kinetic energy due to the 3 decimals limit in the velocities PDB file

2) the vdw energies will not be identical because for periodic systems AMBER introduces a correction term for the van der Waals that is a function of preassure and energy (vdwmeth=1), while NAMD does not. See this link for further details:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/10483.html

 

If you want to run metadynamics with NAMD, all you have to do is:

1) include these lines in your MD configuration file:

colvars on
colvarsConfig colvars_dihedral.conf        # colective variable configuration file
#colvarsInput meta_3.restart.colvars.state # COMMENT OUT UNLEES YOU RESTART A JOB

2) Create a colvars configuration file.

This is an example for distance constraint: