[gmx-users] secondary structure analysis

[Joe Jordan]

Have you tried running the dssp command on a pdb file to ensure that it is
working as intended? FYI 4.5.5 is no longer supported so you may want to
consider upgrading to (the much faster) gromacs 2018.

On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM <islamshahee at gmail.com>
wrote:

> i have installed dssp2.04 in usr/local/bin.
>
> On 5/16/18, Joe Jordan <e.jjordan12 at gmail.com> wrote:
> > You have to point to where you have dssp installed. This may require you
> to
> > install dssp.
> >
> > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM <islamshahee at gmail.com>
> > wrote:
> >
> >> i want calculate the secondary structure of protein in gromacs.but
> >> when i am using this command
> >>
> >> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
> >>
> >> getting this error
> >> Program do_dssp, VERSION 4.5.5
> >> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c,
> line:
> >> 572
> >>
> >> Fatal error:
> >> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7 >
> >> /dev/null 2> /dev/null
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >>       how i will solve this problem.please help me
> >> --
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> >
> >
> >
> > --
> > Joe Jordan
> > --
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-- 
Joe Jordan