Amber to mol2 (protein)

From Rizzo_Lab
Revision as of 16:45, 25 January 2010 by Sudipto (talk | contribs)
(diff) ←Older revision | view current revision (diff) | Newer revision→ (diff)
Jump to: navigation, search

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.

Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=Amber_to_mol2_(protein)&oldid=5481"