wat2polar

Usage

cg_spica map2cg SPICA_PDB pSPICA_PDB

Description

wat2polar converts SPICA CG water to pSPICA polar CG water. SPICA CG ions are also converted to pSPICA’s. This program recognizes the residue names WAT or TIP3 as SPICA CG water, and the residue names SOD and CLA as SPICA CG ions, which are given in a CG configuration file in the PDB format. The residue name of SPICA CG water is converted to PWAT of pSPICA water.

The pSPICA water is created by randomly adding a site at 1.1 A away from the center of the SPICA water without energy minimization. The center and the added sites become the WO and WH segments of the pSPICA water, respectively.

Example

cg_spica map2cg dopc.cg.pdb p_dopc.cg.pdb

_images/wat2polar_example.jpg

dopc.cg.pdb p_dopc.cg.pdb

Positional args

SPICA_PDB [<.pdb>]

Input SPICA configuration

pSPICA_PDB [<.pdb>]

Output pSPICA configuration after the above conversion