Topsolsol: Difference between revisions
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Navigation: [[Documentation]] / [[Commands]] / [[topsolsol]] | Navigation: [[Documentation]] / [[Commands]] / [[topsolsol]] | ||
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<div style="text-align: center">topsolsol: version 2. | <div style="text-align: center">topsolsol: version 2.204.c62bd73(2018-07-04 10:11) [CATs - Conversion And Analysis Tools]</div>'''Name''' | ||
<span style="margin-left: 15px;">topsolsol</span> | <span style="margin-left: 15px;">topsolsol</span> | ||
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'''Description''' | '''Description''' | ||
<p style="text-indent: 1em; text-align: justify;">Analyse solute/solvent contacts according to Delaunay triangulation among the system atoms. The solvent residues are discrimated into directly bound, first, second, third, and fourth solvation layers. The tringulation is created as follows:<br /><br />topcrd2crd --output rbox topology.parm7 coords.rst7 coords.rbox<br />cat coords.rbox | qdelaunay i TO output | <p style="text-indent: 1em; text-align: justify;">Analyse solute/solvent contacts according to Delaunay triangulation among the system atoms. The solvent residues are discrimated into directly bound, first, second, third, and fourth solvation layers. The tringulation is created as follows:<br /><br />topcrd2crd --output rbox topology.parm7 coords.rst7 coords.rbox<br />cat coords.rbox | qdelaunay i TO output</p> | ||
'''Arguments''' | '''Arguments''' | ||
Revision as of 09:20, 4 July 2018
Navigation: Documentation / Commands / topsolsol
topsolsol: version 2.204.c62bd73(2018-07-04 10:11) [CATs - Conversion And Analysis Tools]
Name
topsolsol
Synopsis
topsolsol [OPTIONS] [--] PARM TRIANGULATION SOLUTE SOLVENT OUTPUT
Description
Analyse solute/solvent contacts according to Delaunay triangulation among the system atoms. The solvent residues are discrimated into directly bound, first, second, third, and fourth solvation layers. The tringulation is created as follows:
topcrd2crd --output rbox topology.parm7 coords.rst7 coords.rbox
cat coords.rbox | qdelaunay i TO output
Arguments
| PARM topology file name
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| TRIANGULATION file name with Delaunay triangulation of the system created by qdelaunay command from QHull package
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| SOLUTE solute definition in ASL mask format
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| SOLVENT solvent definition in ASL mask format
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| OUTPUT file name with output masks defining solvent layers around solute
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Options
| -r, --ratio DOUBLE directly bound solvent ratio (Default: 0.2)
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| --directnotsolvent do not use direct as solvent
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| -v, --verbose increase output verbosity
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| --version output version information and exit
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| -h, --help display this help and exit
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