ADL: Re: segmentation

swayam prakash panda swayam_22 at rediffmail.com
Tue Sep 7 19:14:17 PDT 2004


  

Dear kay
         open ~./bashrc file in vi editor and type a line 
ulimit -s unlimited

then save this bashrc file 
and in command promt type source ~./bashrc
then it will work go to autodock webpage and click for faq(frequently asked question) it is written there
urs 
swayam

On Wed, 08 Sep 2004 autodock-request at scripps.edu wrote :
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>Today's Topics:
>
>    1.  ADT and 'source install.csh' for OS X v.10.3 (Philip Crawford)
>    2.  Increasing Number of Atom Types (Michael Ivery)
>    3.  segmentation fault with stacksize unlimited (Kay Gottschalk)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 7 Sep 2004 09:54:11 +1000
> From: "Philip Crawford" <p.crawford at unsw.edu.au>
>Subject: ADL: ADT and 'source install.csh' for OS X v.10.3
>To: <autodock at scripps.edu>
>Message-ID: <000001c4946c$ce6f3570$17335e81 at medicine.domain>
>Content-Type: text/plain;	charset="us-ascii"
>
>Hi. I've just been looking at other things related to autodock and noticed
>in:
>http://www.scripps.edu/pub/olson-web/doc/autodock/faq.html#SEGFAULT
>that Mac OS-X 10.3 now uses the "bash" shell by default, not the c-shell.
>The page referenced tells you how to identify the shell you are using and
>where to place the command to modify stack size.
>
>Cheers,
>
>Philip Crawford
>__________________________________________________
>Philip Crawford, B. Comp. Sc., MIEEE
>School of Medical Sciences
>The University of NSW
>Phone: +61-2-9385 2564
>Mobile: +61-419-294 698
>Fax: +61-2-9385 1059
>Email: p.crawford at unsw.edu.au
>__________________________________________________
>
>
>
>------------------------------
>
>Message: 2
>Date: Tue, 7 Sep 2004 14:15:10 +1000
> From: Michael Ivery <michaeli at pharm.usyd.edu.au>
>Subject: ADL: Increasing Number of Atom Types
>To: autodock at scripps.edu
>Message-ID: <820D39AB-0084-11D9-9704-0003933DA89C at pharm.usyd.edu.au>
>Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>Dear All,
>
>I would appreciate information on increasing the max number of atom
>types allowed in Autodock I have tried recompiling altering the
>Max_MAPS and ATOM_MAPS variables and then recompiling.  This gives an
>error
>
>ranlib -s libad.a
>ranlib: -s: No such file or directory
>make: *** [libad.a] Error 9
>
>Any advice at how I can overcome this problem would be greatly
>appreciated.
>
>Best Wishes
>
>Michael Ivery
>
>
>
>------------------------------
>
>Message: 3
>Date: Tue, 7 Sep 2004 15:57:49 +0300
> From: Kay Gottschalk <kay.gottschalk at weizmann.ac.il>
>Subject: ADL: segmentation fault with stacksize unlimited
>To: autodock at scripps.edu
>Message-ID: <85CAAF2D-00CD-11D9-B4D5-000A9599B076 at weizmann.ac.il>
>Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>Hi there,
>
>I am getting a segmentation fault when using autogrid3 on OS X, with
>stacksize at max (65536 kbytes). The output of the log-file until the
>crash looks rather o.k., I think:
>Atom no. 9607,  " C  "  at (-43.700, -6.565, 4.582),   was assigned
>atom type 1, "C".
>Atom no. 9608,  " O  "  at (-44.811, -6.176, 4.134),   was assigned
>atom type 3, "O".
>Atom no. 9609,  " OXT"  at (-43.078, -5.988, 5.514),   was assigned
>atom type 3, "O".
>
>Maximum partial atomic charge found = +0.814 e
>Minimum partial atomic charge found = -0.867 e
>
>Atom    Atom    Number of this Type
>Type     ID      in Macromolecule
>____    ____    ___________________
>   1       C                5027
>   2       N                1332
>   3       O                1490
>   4       S                  47
>   5       H                1713
>   6       X                   0
>   7       M                   0
>
>Total number of atoms :         9609 atoms
>Total charge :                  -9.00 e
>
>
>Macromolecule coordinates fit within the following volume:
>
>
>Any ideas?
>Thanks,
>Kay
>
>
>
>------------------------------
>
>________________________________________________
>--- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
>End of autodock Digest, Vol 6, Issue 4
>**************************************





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