VMD-L Mailing List

From: Tim Lo (timlo_at_hku.hk)
Date: Thu Sep 18 2014 - 20:19:10 CDT

Hi Aryan,

To construct a CNT, using Nanotube Builder plugin is a convenient
method. Since the CNT is cylindrical but not planar, improper terms are
not needed.

To solvate a system comprised of two molecules (in this case, the CNT
and the protein), I always merge them before using Solvate plugin to add
the solvent box. I like using "mergemols", which is written on top of
"topotools", to merge molecules. Two or more molecules can be merged
together by one script easily. Read the details in Axel's website:
https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-mergemols-list-of-molecule-ids-

With your own effort, I am sure you will be able to achieve your aim
very soon.

Cheers,
Tim
Research Assistant
The University of Hong Kong

On 2014/9/19 上午 03:44, Aryan Vahedi-Faridi wrote:
> Hi,
>
> My name is Aryan Vahedi and I am a graduate at Morgan State University
> in Baltimore, MD. I have been trying to learn VMD and NAMD as best I
> can but still am unable to understand how to set up a simulation with
> a carbon nanotube and protein present. Could someone instruct me on
> the proper procedure to do this? Here is what I have been able to do
> so far:
>
> -Created a PSF and PDB for a carbon nanotube made by the nanotube
> builder that comes with VMD. (Is this alright? Or do I need to use a
> program like 'Nanotube Modeler'?)
>
> -Created a PSF and PDB for the protein in question (GFP in this case,
> also did it for each chain of GFP)
>
> -Made Solvated (Water Box. 0.2 M NaCl) pdb and psf files respectively
> for proteins (have not yet done this for the carbon nanotubes)
>
> I guess my question is do I need to merge the molecules (CNT and
> loaded protein) prior to running the simulation? If not, how do I
> solvate the molecule so that the water box is applied to both at the
> same time? It seems I do not understand the fundamental procedure to
> use when setting up a simulation between two molecules such as a
> protein and carbon nanotube. I would like to run general
> tutorial-suggested analysis once the simulation is complete. I am
> starting with local resources (6-core Athlon) but should have access
> to University computing resources in the future.
>
> Thank you for any help it is greatly appreciated!
>
> Best,
> Aryan
> Morgan State University