Amber to mol2 (protein)

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.