[gmx-users] secondary structure query

Soham Sarkar soham9038 at gmail.com
Tue Jun 12 16:08:33 CEST 2018

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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