[Dock-fans] sphgen problem

William Joseph Allen william.joseph.allen at gmail.com
Mon Nov 26 09:27:51 PST 2012


Hi Fabian,

I have not tried sphgen_cpp, but I just downloaded 1f1t from the PDB,
deleted the waters / ions, generated a surface in chimera, wrote the dms,
and ran sphgen without any problem. Here is what my INSPH file looked like:

1f1t.dms
R
X
0.0
4.0
1.4
1f1t.sph

How did you go about preparing the dms?

Have you tried running sphgen on any other system?

Joe Allen



On Mon, Nov 26, 2012 at 4:37 AM, Fabian Glaser <fabian.glaser at gmail.com>wrote:

> Thanks Maciek,
>
> I tried, but I got compilation errors, I tried on my Mac OSX, I guess it
> is not a 64 bit code?
>
> g++ -g -Wall -pedantic -O4  -c main.cpp
> g++ -g -Wall -pedantic -O4  -c Sphere.cpp
> g++ -g -Wall -pedantic -O4  -o ./sphgen_cpp ./obj/main.o ./obj/Sphere.o
> ld: in ./obj/main.o, could not parse object file ./obj/main.o: Malformed
> metadata record for architecture x86_64
> collect2: ld returned 1 exit status
> make: *** [sphgen_cpp] Error 1
>
> Any suggestion?
>
> Thansk,
>
> Fabian
>
> On Nov 26, 2012, at 11:27 AM, Maciek Wójcikowski wrote:
>
> > Try C version of sphgen.
> http://dock.compbio.ucsf.edu/Contributed_Code/sphgen_cpp.htm
> >
> > ----
> > Pozdrawiam,  |  Best regards,
> > Maciek Wójcikowski
> > maciek at wojcikowski.pl
> >
> >
> >
> > 2012/11/26 Fabian Glaser <fabian.glaser at gmail.com>
> > Hi,
> >
> > I get the following error with sphgen when running on clean 1f1t (no
> ions, no water no ligands):
> >
> > At line 157 of file sphgen.f
> > Fortran runtime error: Bad real number in item 1 of list input
> >
> > What is the problem, and how can it be corrected?
> >
> > Thanks!
> >
> > Fabian
> >
> >
> > _______________________________
> > Fabian Glaser, PhD
> > Bioinformatics Knowledge Unit,
> > The Lorry I. Lokey Interdisciplinary
> > Center for Life Sciences and Engineering
> >
> > Technion - Israel Institute of Technology
> > Haifa 32000, ISRAEL
> > fglaser at technion.ac.il
> > Tel:    +972 4 8293701
> > Fax:   +972 4 8225153
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> >
>
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-- 
William Joseph Allen, Ph.D.
Robert C. Rizzo Research Group
Department of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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