Package: acpype
ACPYPEAnteChamber PYthon Parser interfacEA tool based inPythonto useAntechamberto generate topologies for chemical
compounds and to interface with others python applications like CCPN and ARIA.acpypeis pronounced asace + pipeTopologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.NB:Topologies generated byacpype/Antechamberare based on General Amber Force
Field (GAFF) and should be used only with compatible forcefields like AMBER and
its variant.Several flavours of AMBER FF are ported already for GROMACS (seeffamber) as well as to XPLOR/CNS (seexplor-nih) andCHARMM.This code is released underGNU General Public Licence V3.See onlinedocumentationfor more.NO WARRANTY AT ALLIt was inspired by:amb2gmx.pl(Eric Sorin, David Mobley and John Chodera)
and depends onAntechamberandOpenBabelYASARA Autosmiles(Elmar Krieger)topolbuild(Bruce Ray)xplo2d(G.J. Kleywegt)For Non-uniform 1-4 scale factor conversion (e.g. if usingGLYCAM06), 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.2019.100241ForAntechamber, 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.2005.12.005WANG, 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.20035If 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:10.1186/1756-0500-5-367and (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:44:3:395Alan Silva, DScalanwilteratgmaildotcomHow To Use ACPYPEIntroductionWe now have an up-to-dateweb serviceatBio2Byte(but itdoes nothave theamb2gmxfunctionality).To runacpype, locally, with its all functionalities, you needANTECHAMBERfrom packageAmberToolsandOpen Babelif your input files are of PDB
format.However, if one wantsacpypejust to emulateamb2gmx.pl, one needs nothing
at all butPython.There are several ways of obtainingacpype:ViaCONDA:(It should be wholesome, fully functional, all batteries included)condainstall-cconda-forgeacpypeViaPyPI:If you're using Linux with Intel processors thenpipinstallacpypeis enough and you should have a complete solution. Oterwise ...(Make sure you haveAmberToolsand, optionally but highly recommended,OpenBabel)# You can use conda to get the needed 3rd parties for examplecondacreate-nacpype--channelconda-forgeambertoolsopenbabel# Or for Ubuntu 20:apt-getinstall-yopenbabelpython3-openbabellibarpack++2-devlibgfortran5

pipinstallacpype# or if you feel daringpipinstallgit+https://github.com/alanwilter/acpype.gitNB:If using OpenBabel python module, it's reallyCRITICALto have it installed in the samePythonenvironment ofacpype.By downloading it viagit:(Make sure you haveAmberToolsand, optionally but highly recommended,OpenBabel)# You can use conda to get the needed 3rd parties for examplecondacreate-nacpype--channelconda-forgeambertoolsopenbabel# Or for Ubuntu 20:apt-getinstall-yopenbabelpython3-openbabellibarpack++2-devlibgfortran5

gitclonehttps://github.com/alanwilter/acpype.gitNB:Using this mode, CHARMM topology files will not be generated.ViaDocker:(It should be wholesome, fully functional, all batteries included)If you have Docker installed, you can runacpype_docker.shby:NOTE: first time may take some time as it pulls theacpypedocker image.On Linux / macOS:ln-fsv"$PWD/acpype_docker.sh"/usr/local/bin/acpype_dockerOn Windows:
Using Command Prompt:In the directory where theacpype_docker.batfile is found:setx/Mpath"%path%;%cd%"Commands:acpype_docker-iCCCC

acpype_docker-itests/DDD.pdb-cgasNB:By installing viacondaor using viadockeryou getAmberTools v.21.11andOpenBabel v3.1.1. OurAmberTools v.21.11is a stripped version from the original containing only the necessary binaries and libraries and comes with thecharmmgenbinary fromAmberTools17in order to generate CHARMM topologies.By installing viapipyou getAmberTools(as described above) embedded. However, the included binaries may not work in your system (library dependencies issues) and with only provide binaries for Linux (Ubuntu20) and macOS (Intel).To Test, if doing viagitAt folderacpype/, type:./run_acpype.py-itests/FFF.pdbIt'll create a folder calledFFF.acpype, and inside it one may find topology
files for GROMACS and CNS/XPLOR.Or using a molecule inSMILESnotation:./run_acpype.py-iCCCC# smiles for C4H6 1,3-Butadiene compoundIt'll create a folder calledsmiles_molecule.acpype.To get help and more information, type:./run_acpype.py-hTo InstallAt folderacpype/, type:ln-fsv"$PWD/run_acpype.py"/usr/local/bin/acpypeThen re-login or start another shell session.If viacondaorpip,acpypeshould be in your$PATH.To Verify with GMXGROMACS < v.5.0cdFFF.acpype/
grompp-cFFF_GMX.gro-pFFF_GMX.top-fem.mdp-oem.tpr
mdrun-v-deffnmem# And if you have VMDvmdem.groem.trrGROMACS > v.5.0cdFFF.acpype/
gmxgrompp-cFFF_GMX.gro-pFFF_GMX.top-fem.mdp-oem.tpr
gmxmdrun-v-deffnmem# And if you have VMDvmdem.groem.trrFor MD, doGROMACS < v.5.0grompp-cem.gro-pFFF_GMX.top-fmd.mdp-omd.tpr
mdrun-v-deffnmmd
vmdmd.gromd.trrGROMACS > v.5.0gmxgrompp-cem.gro-pFFF_GMX.top-fmd.mdp-omd.tpr
gmxmdrun-v-deffnmmd
vmdmd.gromd.trrTo Emulateamb2gmx.plFor any givenprmtopandinpcrdfiles (outputs from AMBER LEaP), type:acpype-pFFF_AC.prmtop-xFFF_AC.inpcrdThe output filesFFF_GMX.groandFFF_GMX.topwill be generated inside folderFFF_GMX.amb2gmxTo Verify with CNS/XPLORAt folderFFF.acpype, type:cns<FFF_CNS.inpTo Verify with NAMDseeTutorialNAMD