ENM

Usage

cg_spica ENM CG_PDB CG_TOP [-maxr <float>] [-kENM <float>] [-pspica] [-v1] [-dssp <string>] [-aapdb <string>]

Description

ENM applies the elastic network model (ENM) to CG configuration and generates topology files to prepare input files for running CG-MD with SPICA. ENM requires values for cutoff length and force constants, specified with the -maxr and -kENM options, respectively. The default values are set to 9.0 A and 1.195 kcal/A²/mol, and these values are used in the SPICA protein model (See the SPICA protein ver1 or SPICA protein ver2 paper).

The SPICA protein ver1 does not have backbone parameters dependent on protein secondary structure. So, when using the ver1 parameter set, add an option -v1 for not applying DSSP.

For SPICA protein ver2, incorporating secondary structure-dependent backbone parameters, the DSSP program and protein atomistic configuration (in PDB format) are needed. -dssp and -aapdb options take a file path to DSSP and the protein PDB, respectively. When DSSP can be used through a command on a console, the -dssp option can be skipped.

Example

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

cg_spica ENM 2mag.cg.pdb 2mag.cg.top.v2 -aapdb 2mag.aa.pdb -dssp /usr/bin/dssp

cg_spica ENM 2mag.cg.pdb 2mag.cg.top.pspica -pspica

protein CG configuration (CPK) applied ENM (red)

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

2mag.cg.top.v1 2mag.cg.top.v2 2mag.cg.top.pspica

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

-kENM <float> (1.195) [kcal/A²]

force constant of harmonic potential for ENM

-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