[gmx-users] secondary structure query

[SHAHEE ISLAM]

The index group contains only residue based protein.


On Jun 12, 2018 7:38 PM, "Soham Sarkar" <soham9038 at gmail.com> wrote:

> Do you have any allien group in your structure? If you have, then remove
> that by indexing.. As per my understanding DSSP is very much residue
> specific. Probably cannot read anything but the biomolecules.
>
> On Tue, 12 Jun 2018, 7:01 pm SHAHEE ISLAM, <islamshahee at gmail.com> wrote:
>
> > hi,
> > i am following this tutorial
> > http://cgmartini.nl/index.php/tutorials-general-introduction/proteins.
> > afrter converting the coarse grained protein to all atom structure by
> > charmm force field,i have gotten the all atom gro file.now i want to
> > analyse the secondary structure of thih gro file.
> > when i am using this command
> > do_dssp -s aa_charmm.gro -n index1.ndx -f dynamic.xtc -sc scount.xvg
> > -o ss.xpm -dt 10
> > the error is
> > Fatal error:
> > Failed to execute command: /usr/local/bin/dssp -na ddVp6nYX ddensUfd >
> > /dev/null 2> /dev/null
> > thanking you
> > shahee
> > --
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