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

Scott Brozell sbrozell at rci.rutgers.edu
Fri Jan 31 00:27:14 PST 2014


Hi,

On Thu, Jan 30, 2014 at 04:14:27PM +0000, msmith at mcdaniel.edu wrote:
> We are so close, but there is still something holding us up. Here is the
> output of 'ls -l dock/bin/sphgen’:
> -rwxr-xr-x  1 root  wheel  33816 Jan 30 09:09 sphgen
> 
> When I try to just run it from the command line without any arguments,
> this is the output. I didn’t expect this to work, but maybe it will
> provide some clue:
> msmithmac:bin marilynsmith$ ./sphgen
> At line 122 of file sphgen.f (unit = 5, file = 'stdin')
> Fortran runtime error: File 'INSPH' does not exist

So sphgen is installed and producing the correct result given that input.

> Then, from within Chimera on the command line within that application, I
> run 'sphgen -i INSPH -o OUTSPH’ and it gives the error:
> Unrecognized command: “sphgen”

You should run that command in a Mac terminal window.

Only STEP 1 OPTION 1 of
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
uses Chimera.  All other steps are run in unix which for Mac is a terminal
window.

scott

> I don’t know exactly what Chimera is trying to do and what kind of
> environment it is trying to execute the sphgen command from, so I don’t
> understand why it’s only seeing the first element of the path instead of
> trying to read the entire path.
> 
> I’m kind of rusty on my Unix knowledge so I’m sorry if there’s something
> easy that I’m missing, but I can’t for the life of me figure it out.
> Thanks again for all of the help you have given me and Marilyn.
> 
> ―Chris
> 
> 
> On 1/29/14, 6:14 PM, "Scott Brozell" <sbrozell at rci.rutgers.edu> wrote:
> 
> >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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