[gmx-users] DSSP

[rama david]

Dear friend,
 I think the VMD can do it.
 Use vmd > extension > analysis > timeline .

It will give the residue with color distinguishing  which are in sec state
with timeframe.
But I dont know will it help in finding the percentage of sec. structure.
Try it and if u find it how to do, post it here so I will also know.


With best regards,
Rama david




On Mon, Aug 25, 2014 at 11:42 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> You could ask for it to be installed?
>
> Mark
>
>
> On Mon, Aug 25, 2014 at 2:01 AM, Nikolaos Michelarakis <nm884 at york.ac.uk>
> wrote:
>
> > Hello,
> >
> > I am trying to do a secondary structure analysis to get the percentages
> of
> > each secondary structure in my protein. I know i can use do_dssp but
> > unfortunately DSSP is not installed on the cluster that i have been using
> > and i do not have the acess to install it. Any other ways to do it? or
> > would anyone be able to run it for me? I need it for 3 structures, for 3
> > different forcefields, 9 structures overall.
> >
> > Thanks a lot,
> >
> > Nicholas
> > --
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