AutoDock Vina is a new program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use. Please find attached the ebuild for AutoDock Vina. Reproducible: Always
Created attachment 202245 [details] autodock_vina-1.0.2.ebuild I am not shure about the RDEPEND! So if someone with a x86_64 only Gentoo could check that to see if these dependencies are required. Kind regards Bjoern Olausson
Vina is now at version 1.0.3 Could you provide the ebuild, please? Or, even better, could you submit the ebuild to the science overlay? Thanks in advance.
Created attachment 216468 [details] autodock_vina-1.0.3.ebuild (In reply to comment #2) > Vina is now at version 1.0.3 > > Could you provide the ebuild, please? > Or, even better, could you submit the ebuild to the science overlay? > > Thanks in advance. > No problem. You could have bumped it by yourself :-) #cp autodock_vina-1.0.2.ebuild autodock_vina-1.0.3.ebuild" Cheers Bjoern
Thanks very much indeed. I commented out the RDEPEND lines in the ebuild on my amd64 box, and apparently vina starts without problems. I haven't used it yet, though, to perform any docking. Is it possible to include the ebuild in the science overlay? === ~ $ vina Missing receptor. Correct usage: Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) Search space (required): --center_x arg X coordinate of the center --center_y arg Y coordinate of the center --center_z arg Z coordinate of the center --size_x arg size in the X dimension (Angstroms) --size_y arg size in the Y dimension (Angstroms) --size_z arg size in the Z dimension (Angstroms) Output (optional): --out arg output models (PDBQT), the default is chosen based on the ligand file name --log arg optionally, write log file Misc (optional): --cpu arg the number of CPUs to use (the default is to try to detect the number of CPUs or, failing that, use 1) --seed arg explicit random seed --exhaustiveness arg (=8) exhaustiveness of the global search (roughly proportional to time): 1+ --num_modes arg (=9) maximum number of binding modes to generate --energy_range arg (=3) maximum energy difference between the best binding mode and the worst one displayed (kcal/mol) Configuration file (optional): --config arg the above options can be put here Information (optional): --help print this message --version print program version ~ $ vina --version AutoDock Vina 1.0.3 (Dec 09, 2009) ~ $ ldd /usr/bin/vina linux-gate.so.1 => (0xf77b8000) libm.so.6 => /lib32/libm.so.6 (0xf775d000) libpthread.so.0 => /lib32/libpthread.so.0 (0xf7744000) libc.so.6 => /lib32/libc.so.6 (0xf75d3000) /lib/ld-linux.so.2 (0xf77b9000) ~ $ ===
New version is 1.1.1. You can't just rename the ebuild because the tarball content changed. Should I open a new bug for the version bump?
(In reply to comment #5) > New version is 1.1.1. I forgot to mention you can now build from source: http://vina.scripps.edu/download.html The changes are here: http://vina.scripps.edu/changes
(In reply to comment #5) > New version is 1.1.1. You can't just rename the ebuild because the tarball > content changed. > > Should I open a new bug for the version bump? > No, just add your ebuild here. I have currently no time to look into this, but sure I would test the ebuild. And while on it, go for the source version. Cheers Bjoern
(In reply to comment #7) > > Should I open a new bug for the version bump? > > > > No, just add your ebuild here. He he :) The only problem is I got no idea how to create an ebuild. I'm a humble physical-chemist, not a programmer. Maybe someone else can volunteer?
(In reply to comment #8) > (In reply to comment #7) > > > Should I open a new bug for the version bump? > > > > > > > No, just add your ebuild here. > > He he :) The only problem is I got no idea how to create an ebuild. I'm a > humble physical-chemist, not a programmer. > > Maybe someone else can volunteer? > Well, this is no excuse :-) I am a Biochemist, nevertheless I wrote several ebuilds, patches and programs to speed up my work-flow and other shortcomings ;-) --> http://olausson.de/scriptarchive/16-modeling --> http://olausson.de/maemo/www2sms So take a small ebuild as template (for example from app-editors/joe) and start you first own template for Vina. The community and I will be glad to help. This is a good starting point: http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=1 Cheers Bjoern
It is OS now and in the tree.
(In reply to comment #10) > It is OS now and in the tree. > Hi Justin, thanks a lot! Cheers Bjoern
