VMD-L Mailing List

From: Naveen BK (naveenbk4717_at_gmail.com)
Date: Tue Oct 15 2019 - 00:17:56 CDT

Dear Tamas,
Thanks for your reply. I want to do the automation of network path analysis
by writing script. I guess the above mentioned script will give what I
want. I will try and get back to you.

Thanks and Regards,
Naveen BK,
MSc in bioinformatics,
+918123474717.

On Tue, Oct 1, 2019 at 10:40 PM Tamas Hegedus <tamas_at_hegelab.org> wrote:

> Hi,
>
> It is not clear what is your real problem.
>
> 1. Network path analysis does not need netwrokSetup; you need subopt
>
> 2. However, for subopt you need the contact.dat as the input and you
> generate it using a tcl script (see below) and config file (as in the
> tutorial) (and you also need carma). You run this tcl script with vmd as
> (use different directory for each of your trajectory):
>
> vmd -dispdev text -eofexit < ./net_input.tcl > net_output.log &&
>
> net_input.tcl:
>
> set DIR /opt/vmd-1.9.3/lib/plugins/noarch/tcl/networkview1.41
> set sfile_list "adjacencyMatrix.tcl communityNetwork.tcl
> networkSetup.tcl networkViewGui.tcl networkView.tcl pkgIndex.tcl
> suboptimalPaths.tcl"
>
> foreach sfile $sfile_list {
> source "$DIR/$sfile"
> }
>
> networkSetup ./network.config
>
>
> If you need further help, let me know
>
> Bests, Tamas
>
> On 10/1/19 11:52 AM, Naveen BK wrote:
>
> Dear all,
> I was conducting network path analysis. I have multiple trajectories and I
> want to do it for all. But I want to run it in command mode with scripts
> but not the way explained in the tutorial. Once I get all the output files
> using scripts then it will be easy to load and visualise. But when I tried
> with command line networkSetup flag was not recognised. Please help me out
> to sort this.
>
>
>
>
> Thanks and Regards,
> Naveen BK,
> MSc in bioinformatics,
> +918123474717.
>
>
>