"This script calculates the binding free-energies for smallest and largest CAVER's tunnels"
Installation procedure:
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If you do not have pod2man:
sudo cpan
> install Pod::Man
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./INSTALL -d dir
-d <v> : Installation directory
-h : help message
Running procedure:
script_post_CAVER.sh -p CAVER_PDB_DIR -i CAVER_OUT_DIR -o OUTNAME -c CPU -a C:N:O -t bottleneck -S sshlogin
-p : "CAVER's md_snapshots DIRECTORY"
-i : "CAVER's out DIRECTORY"
-o : "Output name"
-c : "Number of CPU (default: 1)"
-a : "Atoms types (default: C:N:O)"
-t : "curvature:length:bottleneck"
-S : "Distribute jobs to remote computers. The jobs will be run on a list of remote computers. (Example: name@nodeXX)"
Atoms types:
H # Non H-bonding Hydrogen
HD # Donor 1 H-bond Hydrogen
HS # Donor S Spherical Hydrogen
C # Non H-bonding Aliphatic Carbon
A # Non H-bonding Aromatic Carbon
N # Non H-bonding Nitrogen
NA # Acceptor 1 H-bond Nitrogen
NS # Acceptor S Spherical Nitrogen
OA # Acceptor 2 H-bonds Oxygen
OS # Acceptor S Spherical Oxygen
F # Non H-bonding Fluorine
Mg # Non H-bonding Magnesium
MG # Non H-bonding Magnesium
P # Non H-bonding Phosphorus
SA # Acceptor 2 H-bonds Sulphur
S # Non H-bonding Sulphur
Cl # Non H-bonding Chlorine
CL # Non H-bonding Chlorine
Ca # Non H-bonding Calcium
CA # Non H-bonding Calcium
Mn # Non H-bonding Manganese
MN # Non H-bonding Manganese
Fe # Non H-bonding Iron
FE # Non H-bonding Iron
Zn # Non H-bonding Zinc
ZN # Non H-bonding Zinc
Br # Non H-bonding Bromine
BR # Non H-bonding Bromine
I # Non H-bonding Iodine
Z # Non H-bonding covalent map
G # Ring closure Glue Aliphatic Carbon # SF
GA # Ring closure Glue Aromatic Carbon # SF
J # Ring closure Glue Aliphatic Carbon # SF
Q # Ring closure Glue Aliphatic Carbon # SF
Option:
-h : help message
Version:
version : 1.0