[gmx-developers] dssp
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jul 9 21:20:51 CEST 2013
On 2013-07-09 16:44, Mark Abraham wrote:
> That would certainly be one way around the problem! :-) Feel free!
>
> Mark
>
> On Jul 9, 2013 9:14 AM, "Alexey Shvetsov" <alexxy at omrb.pnpi.spb.ru
> <mailto:alexxy at omrb.pnpi.spb.ru>> wrote:
>
Alternative would be to move gromacs functionality into dssp or make a
separate tool within gromacs under a license compatible to dssp and
which is built optionally only (when the modern compilers and boost are
present).
> Hi all!
>
> I had some plans about writing dssp tool for gromacs using c++
> gromacs api for it, is it still needed?
>
> Mark Abraham писал 09-07-2013 00 <tel:09-07-2013%2000>:28:
>
> Gert and I have had some discussion off list. DSSP is available
> under
> the Boost license, which is probably fine to work with LGPLv2.1
> (but I
> haven't looked into details). It turns out the DSSP webpage was in
> need of an update - the new source is indeed freely available. It's
> under 100K, too, so that could be acceptable IMO.
>
> Unfortunately, it requires C++0x and four link-time Boost libraries,
> which is rather beyond the planned requirements for GROMACS 5.0
> (C++98
> and very limited include-only Boost libraries). In theory, we could
> detect all that (or just try it and see) to do an optional internal
> build of dssp, but I think there are probably too few users with all
> the dependencies satisfied who want do_dssp and who would otherwise
> have generated email traffic through being unable to download a
> binary
> or set an environment variable.
>
> Debian and Gentoo have new-generation dssp pacakges, so it is
> reasonable to add the couple of lines of CMake detection for the
> dssp
> or mkdssp executables in the obvious places, rather than hard-code
> /opt/local/bin/dssp (or whatever we do now). We could have a CMake
> option (off by default) to download and install a dssp binary,
> but I'm
> not very keen on that.
>
> Mark
>
>
> On Mon, Jul 8, 2013 at 5:32 PM, Mark Abraham
> <mark.j.abraham at gmail.com <mailto:mark.j.abraham at gmail.com>> wrote:
>
> 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 <mailto: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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>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
> Gatchina, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexxyum at gmail.com <mailto:alexxyum at gmail.com>
> mailto:alexxy at gentoo.org <mailto:alexxy at gentoo.org>
> mailto:alexxy at omrb.pnpi.spb.ru <mailto:alexxy at omrb.pnpi.spb.ru>
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>
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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