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shell. It reads an input parameter file containing field/value pairs: file containing the names of the computers (nodes) to be used

...2 file. Atom and bond types are assigned using the DOCK 4 atom/bond typing parameter files. ...ite molecules to files whose names are formed using the output_file_prefix parameter. DOCK will always write out a scored molecules output file, which contains

...ord, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record. For extensive details on the MOL2 format, as well as example files, please refer to the Tripos web site documentation (http://www.tripos

...for qsub, input file, the function script, parameters for the function. A example is shown below. ...input.txt \ # The input file names and directory

(A) more stringent on keeping original atom names, and To generate the necesary cofactor parameter file issue the following command:

...aracter string that contains one or more patterns that match a set of atom names in a molecule. Atom expressions contain three substrings separated by colon #Select all atoms with names C, CA, N or O in all residues in all strands (typically the peptide backbon

# The outputs are: parameter topology file (prm7) and a coordinate file (rst7) # runs tleap and converts parameter and coordinate restart file back into pdb file

...for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to <tt>getxpdb.pl name_e ...for a different subset of the molecules, first create the list of molecule names plus their energies (on one line) and then feed it to '<tt>getxpdb.pl name_

DOCK must be run command line from a standard unix shell. It reads a parameter file containing field/value pairs using the following command: -machinefile #simple text file containing the names of the computers (nodes) to be used

...led by typing the path to the executable followed by the name of the input parameter file (can be anything, by default inhier). Logical keywords (procedures) c ...do not allow for solvation values and preserve the input residue and atom names. If this option is true, solvation correction should be false; comment out

For example, you might want to modify the the energy threshold maximum that controls po Another parameter to consider changing might be the heavy atom count maximum:

# This parameter set the number of parallel installation processes. # Enabling the WINDOWS_SUPPORT, recommends the following parameter.

Nir and trent got the parms from gaff and change the names, for thio-ether These parameter values were taken from the gaff force field (/nfs/soft/amber/amber14/dat/le

# The outputs are: parameter topology file (prm7) and a coordinate file (rst7) # runs tleap and converts parameter and coordinate restart file back into pdb file