m-hakmi / amber-dyes Goto Github PK

The files in this Folder under GNU Lesser General Public License (LGPL) Version 2.1 contain the AMBER-DYES Force Field Parameters [Graen et al. (20014) JCTC (dx.doi.org/10.1021/ct500869p)] in combination with the AMBER99sb Protein Force Field [Hornak et al. (2006). Proteins 65, 712-725] for the Gromacs 4.5/4.6/5.0 Molecular Dynamics Program [http://www.gromacs.org/]

USAGE:
The force field can be used like any gromacs force field by placing the folder amber99sb_dyes.ff into the share/gromacs/top folder under the local gromacs install, or redirecting the GMXLIB path to the location of the folder by setting
export GMXLIB=PATHTOFOLDER/amber99sb_dyes.ff
or by placing the amber99sb_dyes.ff folder in the current working directory together with the PDB and .mdp files.
To use the force field, prepare your protein PDB file in VMD or PYMOL by attaching labels from the PDB_structures folder to your protein. All supported labels can be found in the PDB_structures folder, though custom dye-linker combinations may also work. For this, do not forget to add your combination to the specbond file. Your protein PDB file can now be processed by pdb2gmx and grompp like any other protein system. An energy minimization prior to production simulations using the robust steepest descent algorithm is recommended.

ORGANIZATION OF THE FILES:
All AMBER-DYES parameters are labeled with "; AMBER-DYES" at the end of the line
Label structures can be found in the PDB_structures folder (attach these labels to your protein).
Charge parameters and residue atom information can be found in the amber99sb_dyes.ff/aminoacids.rtp.
Bonded and nonbonded parameters are located in amber99sb_dyes.ff/ffbonded.itp and amber99sb_dyes.ff/ffnonbonded.itp, respectively.
Atom types are located in amber99sb_dyes.ff/atomtypes.atp