Difference between revisions of "Amber to mol2 (protein)"
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set scriptdir = "home/goyal/RCR/projects_BNL/flu/zzz.scripts.amber | set scriptdir = "home/goyal/RCR/projects_BNL/flu/zzz.scripts.amber | ||
${scriptdir}/zzz.leap2mol2.perl ${system}.rec.gas.min.rst ${system}.rec.gas.leap.parm ${system}.rec.min.mol2 >> ${system}.report.txt | ${scriptdir}/zzz.leap2mol2.perl ${system}.rec.gas.min.rst ${system}.rec.gas.leap.parm ${system}.rec.min.mol2 >> ${system}.report.txt | ||
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| + | This script maps amber atom types to sybyl mol2 atom types. Currently, only atom types for standard amino acids are supports. Do not use this script for small molecules, as the atom types will not be mapped correctly. This script cannot assess bond orders, and sets all bond orders to 1 (single bonds). This is fine for docking and visualization. | ||
Latest revision as of 16:45, 25 January 2010
Use Sudipto's perl script
set scriptdir = "home/goyal/RCR/projects_BNL/flu/zzz.scripts.amber
${scriptdir}/zzz.leap2mol2.perl ${system}.rec.gas.min.rst ${system}.rec.gas.leap.parm ${system}.rec.min.mol2 >> ${system}.report.txt
This script maps amber atom types to sybyl mol2 atom types. Currently, only atom types for standard amino acids are supports. Do not use this script for small molecules, as the atom types will not be mapped correctly. This script cannot assess bond orders, and sets all bond orders to 1 (single bonds). This is fine for docking and visualization.
