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)