[Dock-fans] help!

Terry Lang terry at cgl.ucsf.edu
Mon Nov 7 10:57:45 PST 2005


Dear Dgwei,

The error that you are getting indicates that the protein is too large
for sphgen to handle. Sphgen can only calculate spheres for up to 99,999
surface points, due to strict formating requirements. To fix the
problem, select a subsection of the protein that still includes the
active site and use that to generate the molecular surface and spheres.

Sincerely,
Terry


dengguo wei wrote:

> hi:
> I am a new user of DOCK5.0. I meet a problem that i don't know the reason.
> I fllowed the mannual of DOCK5.2.0, and just changed the pdb(1FJS.pdb)
> in the mannual to
> the pdb of mine, but when i came to run sphgen simply by typing
> ¡°sphgen¡± in the unix shell, the
> program began to run, and half an hour later, error occure"
> sphgen
> #####
> fmt: read unexpected character
> apparent state: unit 2 named temp2.sph
> last format: (2I5,F8.4,I8,4F12.6)
> lately reading sequential formatted external IO
> Aborted
> ###
> There is some imformation in the OUTSPH file
> ####
> density type = X
> reading 1HS6_DHET.ms type R
> # of atoms = 4876 # of surf pts = *****
> finding spheres for 1HS6_DHET.ms
> dotlim = 0.000
> radmax = 4.000
> Minimum radius of acceptable spheres?
> 1.39999998
> output to 1HS6_DHET.sph
> error reading temp2.sph
> 0 70 1.7940 100333 0.204898 32.794994 42.519810 86.566956
> ####
> There are some stange in the temp2.sph, such as
> 99975 472 1.4129 100332 0.458686 32.858223 43.209953 86.896088
> 99982 472 1.4001 101073 0.180901 31.778866 43.969215 86.324226
> 99984 472 1.7940 100333 0.204898 32.794994 42.519810 86.566956
> ***** 473 1.3999 100440 0.060653 39.895714 44.685001 89.402756
> ***** 473 1.4014 101374 0.015855 37.601055 44.066299 92.340057
> ***** 473 1.4960 101349 0.485863 38.062412 44.551533 92.240059
> ***** 473 1.5897 100512 0.256026 39.676300 44.985138 90.693649
> why did the "***" appear?
> I have run it several times, but the error is the same.
> I wonder if some friends would give me a help?
> Thank you very much!
> dgwei
>
>------------------------------------------------------------------------
>
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>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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