[Dock-fans] Segmentation fault, need quick help.

RKH Liyanage rkhliyanage at gmail.com
Sat Apr 22 10:39:45 PDT 2017


Hi

*Thank you very much for your reply. *
Yes I followed this same tutorial you have given below.

However it did not contain following files.

vdw_defn_file ../zzz.parameters/vdw_AMBER_parm99.defn

flex_defn_file ../zzz.parameters/flex.defn

flex_drive_file ../zzz.parameters/flex_drive.tbl

So I had to download these online.
I'm not sure about their content that's why I thought maybe these files
caused the fault.

Please let me know your thoughts.

Regards.


On 22 April 2017 at 20:51, Trent E. Balius <tbalius at aol.com> wrote:

> Hi,
>
> I suspect that the issue is one of the input files.
> How did you prepare your mol2 file?
>
> I would suggest that you do the following tutorial and use it as a
> reference to help debug what is wrong.
>
> http://ringo.ams.sunysb.edu/index.php/2015_DOCK_tutorial_
> with_Poly(ADP-ribose)_polymerase_(PARP)
> http://ringo.ams.sunysb.edu/index.php/DOCK_Tutorials
>
> Also runing dock with the verbose flag might help pinpoint were thing are
> going wrong.
>
> I hope this helps.
>
> Trent
>
> ======================================
> Trent E. Balius, PhD
> Postdoc, Shoichet Lab,
> Dept. Pharm. Chem., UCSF
> Phone: (415) 514-4253
> URL: http://docking.org/~tbalius
> ======================================
>
>
> -----Original Message-----
> From: RKH Liyanage <rkhliyanage at gmail.com>
> To: dock-fans <dock-fans at docking.org>; dockdev <
> dockdev at mailman.docking.org>
> Sent: Sat, Apr 22, 2017 1:24 am
> Subject: [Dock-fans] Segmentation fault, need quick help.
>
> Hi
> I had a an error called segmentation fault when doing energy minimization.
> These are the terminal details.
> https://docs.google.com/document/d1uBfbuddvQSCUTbBIsbV8rhI7A
> ltk_VFs_sX42IiGjU/edit?usp=sharing
> I have attached the input files.
> * I'm not sure about the flex.defn and flex_drive.tbl files.*
> Please have a look and I need urgent advice.
> Thanks
> Regards
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://mailman.docking.org/mailman/listinfo/dock-fans
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20170422/fbb0530d/attachment.html 


More information about the Dock-fans mailing list