map2cg¶

Usage¶

cg_spica map2cg AA_PDB CG_PDB [-json <jsonfile>] [-nodelwat] [-verbose <int>]

Description¶

map2cg performs CG mapping, which converts AA coordinates to CG coordinates. This program requires a json formatted file with CG mapping information contained in the spica-tools/src directory. With the -json option, you can specify other json files to be used for mapping.

Example¶

cg_spica map2cg dopc.aa.pdb dopc.cg.pdb

_images/map2cg_example.jpg

dopc.aa.pdb dopc.cg.pdb

Positional args¶

AA_PDB [<.pdb>]: Input all-atom configuration
CG_PDB [<.pdb>]: Output coarse-grained configuration

Optional args¶

-json <jsonfile> (src/spica_top.json): Input json file for CG mapping
-nodelwat (off): Not delete excess CG water due to CG ion mapping
-verbose <int> (1): Activate verbose logging (0: off, 1: on)