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

Justin Lemkul jalemkul at vt.edu
Thu Feb 12 13:44:13 CET 2015

On 2/11/15 11:29 PM, soumadwip ghosh wrote:
> 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.

Generate topologies for the nucleic acid and CNT independently; this will give 
you two topol.top files.  Remove the system-level directives to make each of 
these an .itp file (see the wiki or manual).  Create a new .top that #includes 
the parent force field, each of the nucleic acid and CNT .itp files, etc.

Position the DNA and CNT in a suitable box using editconf independently (using 
rotation and translation options as needed to create the desired orientation), 
then concatenate the coordinate files.  At this point, you'll have a CNT and DNA 
in a box, with no solvent.  From here on, solvating, adding ions, etc. is the 
same as any simple system.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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