[gmx-users] Simulation of Carbon nanotube

[Justin Lemkul]

On 6/22/17 6:59 AM, Nikhil Maroli wrote:
> Dear Justin,
> I have generated topology for CNT using gmx x2top. There is cyclic peptide
> nanotube wrapped over the CNT (eight CP rings in equal intervals) otherwise
> let's say, CNT is inserted into the Cyclic peptide nanotube. I wanted to
> put the whole system into the lipid bilayer. I was using charmm-gui for the
> input generator since it provides easy hand on CPN, So is it possible to
> convert the CNT topology which generated with gmx x2top to 'Topology and
> Parameters' for charmm-gui (*.rtf and *.prm)?

Possibly, but I've never tried it.  Assuming it's an "infinite" molecule, the 
periodic bonding could be tricky.  You may just want to build the membrane and 
then write a little script to carve out a cylinder of suitable size later, and 
overlay your existing coordinates.  Probably a lot less effort, in the end.

-Justin

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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
http://mackerell.umaryland.edu/~jalemkul

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