ADL: Re: segmentation

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Tue Sep 7 22:47:28 PDT 2004


Hi there,
thanks for your reply. Of curse I checked the FAQ before writing my 
question. Therefore, I already did put 'limit stacksize unlimited' into 
my .cshrc, but still I get the same error. I guess my email wasn't 
clear about this.
Best regards,
Kay.

On Sep 8, 2004, at 5:14 AM, swayam prakash panda wrote:

>
>
> 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
>> **************************************
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- 
> http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
>
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Rehovot
Israel




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