Go

Usage

cg_spica Go CG_PDB CG_TOP [-maxr <float>] [-eps <float>] [-pspica] [-v1] [-dssp <string>] [-aapdb <string>]

Description

Go applies the Go-like model to protein CG configuration and generates topology files to prepare input files for running CG-MD with SPICA. Go requires values for cutoff length and interaction energy, specified with the -maxr and -eps options, respectively. The default values are set to 9.0 A and 1.5 kcal/mol. The other options such as -dssp and -aapdb are the same as the ENM command.

Please note that the SPICA protein with the Go-like model has not been published yet.

Example

cg_spica Go 2mag.cg.pdb 2mag.cg.top.v1.Go -v1

cg_spica Go 2mag.cg.pdb 2mag.cg.top.v2.Go -aapdb 2mag.aa.pdb

2mag.cg.pdb 2mag.aa.pdb

2mag.cg.top.v1.Go 2mag.cg.top.v2.Go

Positional args

CG_PDB [<.pdb>]

Input protein CG configuration

CG_TOP [<.top>]

Output SPICA topology

Optional args

-maxr <float> (9.0) [A]

cutoff length for applying ENM

-eps <float> (1.5) [kcal/mol]

interaction energy of applied Go-like model

-pspica (off)

Assign partial charge (0.5590) for pSPICA FF (default: 0.1118, for SPICA FF)

-v1 (off)

Generate topology file for SPICA ver1, not considering backbone parameters dependent on protein secondary structure

-dssp <string>

File path to the DSSP program

-aapdb <string>

Atomistic protein configuration for applying DSSP