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MacroModel Coordinate Scan

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

The Coordinate Scan panel is used to perform a coordinate scan of one or two coordinates of the same type (distance, angle, or dihedral) on the input structures.

Backend implementation

scripts/mmodCLI.py run by cmdRunner.py
The script mmodCLI.py is passed to cmdRunner.py to implement this node.
utilities/structconvert is then applied to the output structures

Options

Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Include Log in output
Include the Macromodel log in the output data table
Force Field
Available force fields: MM2, MM3, AMBER, OPLS, AMBER94, MMFF, MMFFs, OPLS_2005 (default)
Solvent
Available Solvents: None (i.e. vacuum), Water
Minimization Algorithm
PRCG, TNCG, OSVM, SD, FMNR, LBFGS, TNCG, Optimal
Electrostatic treatment
Force field defined (default), distance dependent, constant dielectric
Dielectric constant
defaults to 1.0
Minimization steps
Maximum number of minimization steps
First coordinate to scan
The first coordinate to scan entered as 2 (distance), 3 (angle) or 4 (dihedral) integers separated by a comma, space or tab.
Column containing first coordinate to scan
Column in input table containing the first coordinate to scan with format as above.
Initial
Specify the initial value for the first coordinate. The default value to enter is 1.0 angstroms for distances and 0.0 degrees for angles and dihedrals.
Final
Specify the final value for the first coordinate. The default value to enter is 10.0 angstroms for distances and 360.0 degrees for angles and dihedrals.
Coordinate type
Select the coordinate type: Distance (two integers), Angle (three integers) and Dihedral (four integers).
Increment
Specify the increment for the first coordinate. An increment can be negative only if the initial value is larger than the final value. The default value to enter is 1.0 angstroms for distance. The minimum angle or dihedral increment is 1 degree, but scans with such fine resolution usually provide less useful information than those with a resolution of 10 degrees. The former also takes more time. The default value to enter for angle or dihedral is 30 degrees.
Use second coordinate for scan
Allows setting of a second coordinate to be scanned, however this must be of the same type as the first i.e. distance, angle or dihedral.
Second coordinate to scan
The second coordinate to scan entered as 2 (distance), 3 (angle) or 4 (dihedral) integers separated by a comma, space or tab.
Column containing second coordinate to scan
Column in input table containing the second coordinate to scan with format as above.
Initial
Specify the initial value for the second coordinate. The default value to enter is 1.0 angstroms for distances and 0.0 degrees for angles and dihedrals.
Final
Specify the final value for the second coordinate. The default value to enter is 10.0 angstroms for distances and 360.0 degrees for angles and dihedrals.
Increment
Specify the increment for the second coordinate. An increment can be negative only if the initial value is larger than the final value. The default value to enter is 1.0 angstroms for distance. The minimum angle or dihedral increment is 1 degree, but scans with such fine resolution usually provide less useful information than those with a resolution of 10 degrees. The former also takes more time. The default value to enter for angle or dihedral is 30 degrees.

Input Ports

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Input data table containing molecules in Maestro format

Output Ports

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Output data table containing minimized molecules in Maestro format

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2
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Developers

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