acpype
The Package
- Requirements:
Python 3.9or higherAntechamber(fromAmberToolspreferably)OpenBabel(optional, but strongly recommended)
This code is released under GNU General Public License V3.
<<< NO WARRANTY AT ALL!!! >>>
It was inspired by:
amb2gmx.pl(Eric Sorin, David Mobley and John Chodera) and depends on Antechamber and OpenbabelYASARA Autosmiles (Elmar Krieger)
topolbuild(Bruce Ray)
xplo2d(G.J. Kleywegt)
For Non-uniform 1-4 scale factor conversion (e.g. if using GLYCAM06), please cite:
BERNARDI, A., FALLER, R., REITH, D., and KIRSCHNER, K. N. ACPYPE update for nonuniform 1-4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS. SoftwareX 10 (2019), 100241. doi: 10.1016/j.softx.2019.100241
For Antechamber, please cite:
WANG, J., WANG, W., KOLLMAN, P. A., and CASE, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling 25, 2 (2006), 247-260. doi: 10.1016/j.jmgm.2005.12.005
WANG, J., WOLF, R. M., CALDWELL, J. W., KOLLMAN, P. A., and CASE, D. A. Development and testing of a General Amber Force Field. Journal of Computational Chemistry 25, 9 (2004), 1157-1174. doi: 10.1002/jcc.20035
If you use this code, I am glad if you cite:
SOUSA DA SILVA, A. W. & VRANKEN, W. F. ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes 5 (2012), 367 doi: 10.1186/1756-0500-5-367
and (optionally)
BATISTA, P. R.; WILTER, A.; DURHAM, E. H. A. B. & PASCUTTI, P. G. Molecular Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease. Cell Biochemistry and Biophysics 44 (2006), 395-404. doi: 10.1385/CBB:44:3:395
Alan Silva, D.Sc. <alanwilter _at_ gmail _dot_ com>
Modules
Constructors to define and store the system's topology |
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