Re: NetworkView plugin for the non-namd trajectories

From: Vlad Cojocaru (
Date: Tue Apr 14 2015 - 10:13:47 CDT

Dear James,

We have a paper just about to be accepted in which we used it for
protein-nucleic acids interactions ...

You don't need covariance with another software. You can create a
surrogate PSF file (from a PDB or amber topology) and convert your AMBER
trajectory to DCD with VMD quite easily (writepsf and animate write
dcd). For the networkview plugin, the info related to force field
parameters in the PSF is not important because the analysis uses
correlations which are obtained from the coordinates ... You just need
the PSF as a match for the DCD.

Don't know which kind of system you are studying but our experience says
that at least in the case of protein-nucleic acids you should play a bit
with the node definition .. The results may depend quite a bit on this.

Hope this helps

On 04/14/2015 04:34 PM, James Starlight wrote:
> Dear NAMD users!
> I wonder to ask whether someone used VMDs NetworkView plugin for the
> analysis of the biosimulations carried out not in NAMD (e,g I'm
> working with Amber outputs now)? From the tutorial
> I've found that to calculate covariance matrix prior to Networks
> calculations some external programs like CARMA are used which directly
> works with the NAMD-like psf topologies. Are there any other
> possibilities to do the same using amber-like inputs topology assuming
> that my trajectory has been converted in DCD? Is it possible to use
> covariance matrix calculated by means of another software e,g g_covar?
> What are the sequence of the steps will be in that case while loading
> it's into VMD?
> Thanks!

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