[gmx-users] Insertion of a carbon nanotube in a system

soumadwip ghosh soumadwipghosh at gmail.com
Thu Feb 12 05:29:16 CET 2015

Dear users,
                  I am currently working in the direction of adsorption of
nucleic acids on the surface of single-wall carbon nanotubes (SWCNT) and I
have made a SWCNT with indices (3,3) using the package Tubegen. What I dont
know is how to insert it in my system containing nucleic acids, solvent and
ions. Is it possible to add the SWCNT just by making the topology by
altering the atom types with the help of pdb2gmx and then add it by using
-ci -nmol options of the genbox? Can I use packmole to generate the initial
structure by putting all the nucleic acis.PDB, SWCNT.PDB and spce.PDB
together? I saw a paper where the ssDNA-SWCNT has been modeled by using
xleap package of AMBER which I dont know how to use. Is there any other
simpler way for the above purpose? I hope I'm not asking for much.

Thanks and regards,
Soumadwip Ghosh
Research Felllow
Indian Institute of Technology, Mumbai

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