• buildCstruct 1.2 (Andrea Minoia, Martin Voegele) Generates atomistic structures of carbon nanotubes (CNTs) or graphite. Can add three different functional groups to the rim (OH, COOH, COO-) of a CNT. Partial charges, if desired, are parameterized for use with the Amber force field. See also https://chembytes.wikidot.com/buildcstruct. License: Free to use, modify and distribute

• acpype.py (Alan Wilter Sousa da Silva) Assigns generalized Amber (GAFF) parameters to organic molecules. This is included only for convenience and was taken unchanged as provided. See also https://www.ccpn.ac.uk/v2-software/software/ACPYPE-folder. License: GNU General Public License V3.

• Two example bash scripts (Martin Voegele) and a folder with ready-to-use example CNTs: The scripts invoke buildCstruct and acpype to generate some example CNTs with various functional groups at the rim. License: Free to use, modify and distribute

• An example simulation set-up for a CNT porin in a lipid membrane for use with the Amber simulation package. This is only to document the set-up process of the simulations and was not tested on any other but MPIBP in-house clusters.

• Python 2.7 and Numpy

(for acpype.py:)

• Antechamber (from AmberTools preferably) version 15(!)

• OpenBabel (optional, but strongly recommended)

If all requirements are fulfilled (see above), no installation is required.

To build your CNT, invoke buildCstruct

./buildCstruct1_2.py -s [armcnt|zigzagcnt] -g [index n] [length in Angstrom] --mol2 [filename].mol2 -f [none|oh|cooh|coo]

To make the CNT topology, invoke acpype (for large systems, this might need a lot of memory)

./acpype.py -i [filename].mol2 -c user 

Both steps are scripted for various CNT geometries in

• maketubes-armchair.sh
• maketubes-zigzag.sh

• M. Vögele, J. Köfinger, G. Hummer: Simulations of Carbon Nanotube Porins in Lipid Bilayers. Faraday Discuss., 2018, Accepted Manuscript, DOI: 10.1039/C8FD00011E
  https://pubs.rsc.org/en/content/articlelanding/2018/fd/c8fd00011e

(buildCstruct)

• A. Minoia, L. Chen, D. Beljonne, L. Lazzaroni: Molecular Modeling Study of the Structure andStability of Polymer/Carbon Nanotube Interfaces. Polymer 53 (2012) 5480-5490

(acpype)

• A. W. Sousa da Silva, W. F. Vranken: ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes 2012, 5:367 doi:10.1186/1756-0500-5-367 https://www.biomedcentral.com/1756-0500/5/367

(Antechamber)

• J. Wang, W. Wang, P. A. Kollman, D. A. Case: Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25, 2006, 247260.
• J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case: Development and testing of a general AMBER force field. Journal of Computational Chemistry, 25, 2004, 1157-1174.