[Dock-fans] Installation of DOCK 6.6 on a Mac

Scott Brozell sbrozell at rci.rutgers.edu
Wed Jan 29 15:14:02 PST 2014


Hi,

Thanks for the report on parser.y.
This has already been fixed in the AmberTools repository which we plan
to sync with Dock in the next release.

If the installation of the utilities finished w/o error then sphgen 
should exist;  what is the output of
ls -l dock/bin/sphgen
?

Did you run the tests ?
An absent sphgen would cause some of the tests to fail.

You may just need to correctly update your path to include dock/bin
or use the full path as above, dock/bin/sphgen.

As far as i know, Chimera does not have a sphgen tool, 
so this tutorial is apt:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm

scott

On Wed, Jan 29, 2014 at 09:20:33PM +0000, msmith at mcdaniel.edu wrote:
> Scott - I cannot thank you enough for your help so far.  Using #2 below we
> got the program and utilities installed.  Installation of the utilities
> gave the following error which Chris fixed by editing
> /usr/local/cvsroot/dock6/src/tleap/parser.y
> 
> by commenting out line 221 since it was giving the error:
> 
> *****************
> parser.y:221:4: error: non-void function 'yyparse' should return a value
> [-Wreturn-type]
>                         return;
> *****************
> So no errors upon installation BUT the command sphgen is not recognized in
> Chimera and a ³which sphgen² give no output.  Any thoughts on this last
> step?  Marilyn
> 
> On 1/28/14, 2:12 PM, "Scott Brozell" <sbrozell at rci.rutgers.edu> wrote:
> >So the gcc and gfortran versions are the same which indicates
> >a different problem than in
> >http://mailman.docking.org/pipermail/dock-fans/2013-December/002868.html
> >
> >In the absence of help from actual mac users, i see 3 options:
> >1.  Double check with a clean rebuild:
> >cd dock/install; make distclean; configure gnu; make install
> >
> >Assuming this fails as below, either of these could be tried:
> >
> >2.  Patch (or hand edit) dock to avoid tnt using the attached
> >no_score_chemgrid.dif:
> >cd dock/src/dock; patch no_score_chemgrid.dif
> >cd dock/install; make distclean; configure gnu; make install
> >
> >3.  Re set up your Mac for scientific computing using a trusted source:
> >http://jswails.wikidot.com/mac-os-x
> >


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