ENM

Usage

cg_spica ENM CG_PDB CG_TOP [-maxr <float>] [-kENM <float>] [-pspica]

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, and these values are ueed in the SPICA protein model (See the protein SPICA paper).

Example

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

_images/ENM_example.jpg

protein CG configuration (CPK) applied ENM (red)

2mag.cg.pdb 2mag.cg.top

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)