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The CgProt software package is a coarse-grained force field for efficient 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.
Version 2.6 coming soon... ask us for a pre-release version.
*Changes for version 2.5 (9/9/21):
-Added divalent calcium cation (type HH) -Added monovalent sodium cation (type POS) -Added chloride anion as NEG site type (see solv.itp) -Added mkions function (v.1) -Tested with Gromacs v.2018
*Changes for version 2.4 (7/8/17): [PeerJ 6:e4230 (2018)]
-Assigned the following site types to match bilayer permeation profiles: 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.
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