CgProt

The CgProt software package is a coarse-grained force field for molecular dynamics simulations of lipid-protein interactions in membrane protein systems. Parameters, scripts, input files, and equilibrated bilayer coordinates are freely available for download to use with the Gromacs simulation package.


*Changes for version 2.4 (7/8/17): [PeerJ 6:e4230 (2018)]


-Assigned the following site types [to match Nature Struct. Biol. 3:842]: Calpha backbone: POL Ala: APOL Asn: POL Lys: POL-POS Asp: POL-NEG Glu: POL-NEG Phe: APOL-APOL-POL Val: APOL-APOL Trp: APOL-POL-APOL-APOL

*Changes for version 2.3 (8/23/16): [AIMS Mol. Sci. 4:352 (2017)]


-Supports peptides of fewer than 4 residues (not capped).
-N/C-termini assigned as POS/NEG sites instead of Calpha site type.
-New site assignments based on PMF in DOPC bilayer [Biophys. J. 94:3393]: -Asn/Gln assigned two polar sites; Cys sidechain assigned as apolar -Trp/Tyr assigned two polar sites (Cgamma and Cepsilon) -Arg assigned two polar sites (Cbeta and Cgamma) and positive Cdelta -Lys assigned two polar sites (Cbeta and new midpoint particle)
-Added offset variable for membrane ndx/tcl files so protein atoms not numbered from 1.

*Changes for version 2.1: [Methods Mol. Biol. 1084:123 (2014)]


-Relaxed stiff bonds > 100 000 kJ mol-1 nm-2 to allow 5fs timestep.

*Changes for version 2.0:


-Includes Cbeta L chirality corrections [MiMB 1084:123]
-Excludes 1,4 nonbonded interactions for which a backbone dihedral exists.
-Removed tabulated bonds.