ADL: can we do...

dharani dharan biodharani at yahoo.co.in
Wed Apr 5 10:22:37 PDT 2006


hi 
  Can we do protein-protein docking with Autodock?
  any research  paper available? 
  please answer
  DHARANI DHARAN
  BIOTECHNOLOGY
  THE NEW COLLEGE
  CHENNAI 
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Today's Topics:

1. segmentation fault with autogrid (J Gill)


----------------------------------------------------------------------

Message: 1
Date: Sun, 2 Apr 2006 22:19:02 -0700 (PDT)
From: J Gill 
Subject: ADL: segmentation fault with autogrid
To: autodock at scripps.edu
Message-ID: <20060403051902.16104.qmail at web38910.mail.mud.yahoo.com>
Content-Type: text/plain; charset=iso-8859-1

Hi,

I am now trying to run autogrid on a redhat enterprise
linux machine in bash shell. I have added 'ulimit -s
unlimited' in .bashrc file. I am still getting
'segmentation fault' error upon running autogrid :(

the gpf file is:

*****************************
receptor 1n81.pdbqs #macromolecule
gridfld 1n81.maps.fld #grid_data_file
npts 125 125 125 # num.grid points
in xyz
spacing 0.502777777777 # spacing(A)
gridcenter 77.709 40.107 47.437 # xyz-coordinates
or auto
types CANOSPHfFcbI #atom type
names
smooth 0.500 #store minimum energy within radius
(Angstroms)
map 1n81.C.map #filename of
grid map
nbp_r_eps 4.00 0.0222750 12 6 #C-C lj
nbp_r_eps 3.75 0.0230026 12 6 #C-N lj
nbp_r_eps 3.60 0.0257202 12 6 #C-O lj
nbp_r_eps 4.00 0.0257202 12 6 #C-S lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
sol_par 12.77 0.6844 #C atomic
fragmental volume, solvation param.
constant 0.000 #C grid map
constant energy
map 1n81.A.map #filename of
grid map
nbp_r_eps 4.00 0.0222750 12 6 #A-C lj
nbp_r_eps 3.75 0.0230026 12 6 #A-N lj
nbp_r_eps 3.60 0.0257202 12 6 #A-O lj
nbp_r_eps 4.00 0.0257202 12 6 #A-S lj
nbp_r_eps 3.00 0.0081378 12 6 #A-H lj
sol_par 10.80 0.1027 #A atomic
fragmental volume, solvation param.
constant 0.000 #A grid map
constant energy
map 1n81.N.map #filename of
grid map
nbp_r_eps 3.75 0.0230026 12 6 #N-C lj
nbp_r_eps 3.50 0.0237600 12 6 #N-N lj
nbp_r_eps 3.35 0.0265667 12 6 #N-O lj
nbp_r_eps 3.75 0.0265667 12 6 #N-S lj
nbp_r_eps 2.75 0.0084051 12 6 #N-H lj
sol_par 0.00 0.0000 #N atomic
fragmental volume, solvation param.
constant 0.000 #N grid map
constant energy
map 1n81.O.map #filename of
grid map
nbp_r_eps 3.60 0.0257202 12 6 #O-C lj
nbp_r_eps 3.35 0.0265667 12 6 #O-N lj
nbp_r_eps 3.20 0.0297000 12 6 #O-O lj
nbp_r_eps 3.60 0.0297000 12 6 #O-S lj
nbp_r_eps 1.90 0.3280000 12 10 #O-H hb
sol_par 0.00 0.0000 #O atomic
fragmental volume, solvation param.
constant 0.236 #O grid map
constant energy
map 1n81.S.map #filename of
grid map
nbp_r_eps 4.00 0.0257202 12 6 #S-C lj
nbp_r_eps 3.75 0.0265667 12 6 #S-N lj
nbp_r_eps 3.60 0.0297000 12 6 #S-O lj
nbp_r_eps 4.00 0.0297000 12 6 #S-S lj
nbp_r_eps 2.50 0.0656000 12 10 #S-H hb
sol_par 0.00 0.0000 #S atomic
fragmental volume, solvation param.
constant 0.000 #S grid map
constant energy
map 1n81.P.map #filename of
grid map
nbp_r_eps 4.10 0.0257202 12 6 #P-C lj
nbp_r_eps 3.85 0.0265667 12 6 #P-N lj
nbp_r_eps 3.70 0.0297000 12 6 #P-O lj
nbp_r_eps 4.10 0.0297000 12 6 #P-S lj
nbp_r_eps 3.10 0.0093852 12 6 #P-H lj
sol_par 0.00 0.0000 #P atomic
fragmental volume, solvation param.
constant 0.000 #P grid map
constant energy
map 1n81.H.map #filename of
grid map
nbp_r_eps 3.00 0.0081378 12 6 #H-C lj
nbp_r_eps 2.75 0.0084051 12 6 #H-N lj
nbp_r_eps 1.90 0.3280000 12 10 #H-O hb
nbp_r_eps 2.50 0.0656000 12 10 #H-S hb
nbp_r_eps 2.00 0.0029700 12 6 #H-H lj
sol_par 0.00 0.0000 #H atomic
fragmental volume, solvation param.
constant 0.118 #H grid map
constant energy
map 1n81.f.map #filename of
grid map
nbp_r_eps 2.65 0.0057469 12 6 #f-C lj
nbp_r_eps 2.40 0.0059400 12 6 #f-N lj
nbp_r_eps 2.25 0.0066379 12 6 #f-O lj
nbp_r_eps 2.65 0.0066379 12 6 #f-S lj
nbp_r_eps 1.65 0.0020938 12 6 #f-H lj
sol_par 0.00 0.0000 #f atomic
fragmental volume, solvation param.
constant 0.000 #f grid map
constant energy
map 1n81.F.map #filename of
grid map
nbp_r_eps 3.54 0.0162608 12 6 #F-C lj
nbp_r_eps 3.29 0.0167954 12 6 #F-N lj
nbp_r_eps 3.15 0.0187852 12 6 #F-O lj
nbp_r_eps 3.54 0.0187852 12 6 #F-S lj
nbp_r_eps 2.54 0.0059400 12 6 #F-H lj
sol_par 0.00 0.0000 #F atomic
fragmental volume, solvation param.
constant 0.000 #F grid map
constant energy
map 1n81.c.map #filename of
grid map
nbp_r_eps 4.04 0.0302197 12 6 #c-C lj
nbp_r_eps 3.79 0.0311999 12 6 #c-N lj
nbp_r_eps 3.65 0.0348827 12 6 #c-O lj
nbp_r_eps 4.04 0.0348827 12 6 #c-S lj
nbp_r_eps 3.04 0.0110335 12 6 #c-H lj
sol_par 0.00 0.0000 #c atomic
fragmental volume, solvation param.
constant 0.000 #c grid map
constant energy
map 1n81.b.map #filename of
grid map
nbp_r_eps 4.17 0.0358776 12 6 #b-C lj
nbp_r_eps 3.92 0.0370508 12 6 #b-N lj
nbp_r_eps 3.77 0.0414166 12 6 #b-O lj
nbp_r_eps 4.17 0.0414166 12 6 #b-S lj
nbp_r_eps 3.17 0.0130977 12 6 #b-H lj
sol_par 0.00 0.0000 #b atomic
fragmental volume, solvation param.
constant 0.000 #b grid map
constant energy
map 1n81.I.map #filename of
grid map
nbp_r_eps 4.36 0.0427235 12 6 #I-C lj
nbp_r_eps 4.11 0.0441342 12 6 #I-N lj
nbp_r_eps 3.96 0.0493465 12 6 #I-O lj
nbp_r_eps 4.36 0.0493465 12 6 #I-S lj
nbp_r_eps 3.36 0.0156073 12 6 #I-H lj
sol_par 0.00 0.0000 #I atomic
fragmental volume, solvation param.
constant 0.000 #I grid map
constant energy
elecmap 1n81.e.map #electrostatic
potential map
dielectric -0.1146 
#<0,distance-dep.diel; >0,constant
#fmap 1n81.f.map #floating grid
# gpf3gen.awk 3.0.5 #

********************
is it something to do with the gpf file?
please help!
regards,
j gill

--- Alexandre Gillet wrote:

> Hi,
> You should try to set the stacksize on your computer
> to be unlimited
> add "limit stacksize unlimited" to your ".cshrc",
> ".tcshrc", or other 
> similar shell-run commands file.
> Alex
> 
> -- 
> o Alexandre Gillet email:
> gillet at scripps.edu
> / The Scripps Research Institute, 
> o Dept. Molecular Biology, MB-5, 
> \ 10550 North Torrey Pines Road, 
> o La Jolla, CA 92037-1000, USA. 
> / tel: (858) 784-2053
> o fax: (858) 784-2860
> 
> 
> 
> 


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