[Dockdev] GBSA problem with Dock5.2_mac

Terry Lang terry at cgl.ucsf.edu
Mon Jul 11 16:54:15 PDT 2005


Dear Suxin,

          Were you able to run the GBSA accessory programs successfully 
before you ran the DOCK calculation?

Thanks,
Terry


Suxin Zheng wrote:

>> *I have download the dock.5.2_mac and run the demo test. While I 
>> found no introduction on GBSA score. And when I try to run the GBSA 
>> score with the demo data, it gave out:
>> *
>
> dock5 -i gbsa_dock.in
> ...
> ...
> Initializing Library File Routines...
> Initializing GB/SA Pairwise Score Routines...
> Initializing Energy Score Routines...
> Reading the energy grid from grid.nrg
> Bus error
>
> Have you used the GBSA score to test the demo data? How to resolved 
> this problem. I have put this question to dock_fan, but with no 
> resolution.
>
> Could you help me to use the GBSA score.
> suxin
>
>> *F**rom: *Suxin Zheng <sxzheng at u.washington.edu 
>> <mailto:sxzheng at u.washington.edu>>
>> *Date: *July 8, 2005 11:39:13 AM PDT
>> *To: *dock-fans at docking.org <mailto:dock-fans at docking.org>
>> *Subject: **GBSA problem with Dock5.2_mac*
>>
>>
>> Hi,
>>
>> I am using the pre-compiled dock5.2 for mac. I have run the demo test 
>> with no GBSA term which is OK. Then I try to use the GBSA score. 
>> First, I build INCHEM for gb and use nchemgrid_GB to generate the 
>> gb_grid. Second build another INCHEN for sa and use nchemgrid_SA to 
>> generate the sa_grid. Then I rebuild the dock.in file for gbsa score 
>> as the attachment. (I found it need to change the gbsa_score_primary 
>> to gbsa_pairwise_score_primary, is it right. I have recompile the 
>> sphgen and grid program.)
>> Then I use: dock5 -i gbsa_dock.in -o gbsa_dock.out
>> it gives out: Bus error when reading the nrg grid.
>>
>> the grid.in, gbsa_dock.in and gbsa_dock.out are enclosed.
>>
>> Could somebody deal with this problem.
>>
>> Thank you
>> suxin
>>
> =
> ------------------------------------------------------------------------
>
>> ----------------------------------------------------------------------
>> Suxin Zheng
>> Box 351700
>> Department of Chemistry, University of Washington
>> Seattle, WA, 98195-1700
>> sxzheng at u.washington.edu <mailto:sxzheng at u.washington.edu>
>>
>>
>>
>>
>
>
>
> =
>
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>
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-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 




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