[gmx-developers] dssp

[Mark Abraham]

Hi Gert, cc gmx-developers,

We do feel your pain - we get such emails too!

Our do_dssp tool requires the user either install dssp as
/usr/local/bin/dssp, or set the DSSP environment variable to point at
the installed dssp binary. This is one source of problems - users
often aren't savvy enough to do either correctly. Another source of
problems has been the change of invocation syntax with newer versions
of dssp. Installations of GROMACS 4.5 and earlier cannot cope with the
newer syntax if that's what is used by the dssp that the user has
installed. Unfortunately we can't do anything about that
retrospectively.

GROMACS 4.6 supports both dssp syntaxes, and defaults to using the new
syntax. This causes problems if they have an old dssp, but that
problem is probably not frequent! Anyway, as installations of earlier
GROMACS and DSSP versions die out, those problems will go away. We
still need a mechanism to find the dssp binary, though, and since
there's no reliable place to look for one at configure or run time,
there's no really good solution.

The solution with the least ongoing impact would be to bundle the dssp
source code and call it directly, which would also make these analyses
much faster for GROMACS users. That would require that we can get and
distribute the dssp source code under a license compatible with ours
(LGPL v2.1). We cannot do so with FFTW source, for example, because
they only make it available under GPL. Just being "open source" is not
enough, unfortunately.

If such a license is not acceptable to you, we could consider an
option for our build system that downloads a Linux binary from your
FTP site and installs it alongside GROMACS. That's similar to an
existing feature we have for letting the user download and build FFTW
as part of the GROMACS build. Such an option would have to be disabled
by default, and so I think that could be more work than its reward.

Regards,

Mark

On Mon, Jul 8, 2013 at 9:08 AM, Bert de Groot <bgroot at gwdg.de> wrote:
> Hi,
>
> I got the message below from Gert Vriend. My impression is that it would be
> easiest to incorporate the new, open source, algorithm of dssp into do_dssp.
> That will alleviate all of the version incompatibility issues, as well as
> file format issues.
>
> cheers
>
> Bert
>
>
>
> About once a week I get mails from people who have difficulties using DSSP.
> Every time it takes me three mails before I found out that this is a Gromacs
> user.
>
> We made a new DSSP about a year ago, and this TOTALLY REWRITTEN DSSP is now
> open source. Would it be possible that anybody from the Gromacs team looks
> at DSSP and tells us what to do to make it usable for the Gromacs community?
>
> I think this is especially important since the PDB format will stop to be
> used by the PDB on 1-1-2014, so everybody MUST start using the new DSSP by
> that time anyway.
>
> Greetings
> Gert
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