json2top

Usage

cg_spica json2top RESNAME [-json <jsonfile>] [-dupang]

Description

json2top generates the topology files needed to setup CG-MD with SPICA. The output is (RESNAME).top, where RESNAME is a mandatory argument to run the program. This command requires a file in json format with CG mapping information, contained in spica-tools/src directory. -json can specify other json files to be used to generate topology files. Angle indices in generated topology files are created based on bond information decribed in the json file. By default, for cyclic molecules, duplicated angle indices are automatically removed. This removal can be turned off with the -dupang option.

NOTE: After generating topology files, please make sure that the bond and angle indices in the file are correct and as expected, especially for molecules containing cyclic groups.

Example

cg_spica json2top POPC

POPC.top

atom     1  POPC    NC    NC   87.1647    0.1118  U
atom     2  POPC    PH    PH   94.9716   -0.1118  U
atom     3  POPC    GL    GL   41.0725    0.0000  U
...

bond     1     2 # NC PH
bond     2     3 # PH GL
...

angle     1     2     3 # NC PH GL
angle     2     3     4 # PH GL EST1
...

Positional args

RESNAME [<string>]

Residue name included in the json file

Optional args

-json <jsonfile> (src/spica_top.json)

Input json file

-dupang (off)

Not delete duplicated angle indices