[Dock-fans] Re: [Dockdev] GBSA problem with Dock5.2_mac

Terry Lang terry at cgl.ucsf.edu
Fri Jul 22 13:16:49 PDT 2005


Dear Suxin,

          We have finalized the bug fix for your problem.  It is posted 
on the web at http://dock.compbio.ucsf.edu/DOCK_5/index.htm.  Please let 
me know if you are still having problems with your calculations.  Thank 
you for supplying your files for debugging purposes!

Sincerely,
Terry


Suxin Zheng wrote:

> Dear Terry,
> I just put some structure and input file. (I just use the demo  
> structure to test the gbsa score). If any files needed I would like  
> to send it.
> suxin
>
> On Jul 18, 2005, at 6:13 PM, Terry Lang wrote:
>
>> Dear Suxin,
>>            I am unable to debug your problem with the information  
>> you have given me.  Can you tar up all of your files and send them  
>> as an attachment?
>>
>> Thanks,
>> Terry
>>
>>
>> Suxin Zheng wrote:
>>
>>
>>>> Dear Terry,
>>>>
>>>> I try to find the problem of my GBSA. While I found maybe my   
>>>> sa_grid.bump file generate wrong. The head of my sa_grid.bump is:
>>>> mac:~/zsx_test/dock5/struct_files sxzheng$ head sa_grid.bmp
>>>> bump map
>>>>    0.400  -3.648  45.910  40.435  79  68  76
>>>> 9001   11 1960*********    4.000    0.000 25
>>>> FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 
>>>> FF FFFFFFFFFF
>>>> FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 
>>>> FF FFFFFFFFFF
>>>> FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF 
>>>> FF FFFFFFFFFF
>>>>
>>>> So when score.cpp read the sa_grid.bump, the variable   
>>>> sa_grid_cutsq, sa_grid_f_scale, sa_rec_solv_rec and  sa_grid_nvtyp  
>>>> are all equal  to zero.
>>>>
>>>> Do you know what's the problem when I generate the sa_grid files.
>>>>
>>>> Suxin
>>>>
>>>
>>>
>>> On Jul 13, 2005, at 1:22 PM, Terry Lang wrote:
>>>
>>>
>>>> Dear Suxin,
>>>>
>>>>          From looking at your files so far, there doesn't seem  to  
>>>> be anything obviously wrong.  I will continue to perform  some  
>>>> diagnostics, but I saw you had to recompile grid and  sphgen.  Can  
>>>> you tell me why you needed to do this?
>>>>
>>>> Thanks,
>>>> Terry
>>>>
>>>>
>>>> Suxin Zheng wrote:
>>>>
>>>>
>>>>
>>>>> Dear Terry,
>>>>> Yes. I have completed the grid with nchemgrid_GB and  
>>>>> nchemgrid_SA   with the individually.
>>>>> First I create a INCHEM(as the attachment INCHEM_gb ), using    
>>>>> "nchemgrid_GB" to generate the GB grid.
>>>>> Secondly,  I create another INCHEM(as the attachment  
>>>>> INCHEM_sa),   using "nchemgrid_SA" to generaate the SA grid.
>>>>>
>>>>> This is the file generated:
>>>>> mac:~/zsx_test/dock5 sxzheng$ ls -l gb* sa*
>>>>> -rw-r--r--   1 sxzheng  sxzheng   413484 Jul 11 17:04 gb_grid.bmp
>>>>> -rw-r--r--   1 sxzheng  sxzheng    27384 Jul 11 17:05 gb_grid.rec
>>>>> -rw-r--r--   1 sxzheng  sxzheng  1633096 Jul 11 17:05 gb_grid.sol
>>>>> -rw-r--r--   1 sxzheng  sxzheng  3266192 Jul 11 17:05 gb_grid.vdw
>>>>> -rwxr-xr-x   1 sxzheng  sxzheng     4581 Jul 10 11:00 gbsa_dock.in
>>>>> -rwxr-xr-x   1 sxzheng  sxzheng     5105 Jul  8 10:27   
>>>>> gbsa_dock.in.bak
>>>>> -rw-r--r--   1 sxzheng  sxzheng     6392 Jul  8 11:27 gbsa_dock.out
>>>>> -rw-r--r--   1 sxzheng  sxzheng   413485 Jul 11 17:08 sa_grid.bmp
>>>>> -rw-r--r--   1 sxzheng  sxzheng    19776 Jul 11 17:08 sa_grid.sas
>>>>> -rw-r--r--   1 sxzheng  sxzheng  2243145 Jul 11 17:08  
>>>>> sa_grid.sasmark
>>>>>
>>>>> then I use: dock5 -i gbsa_dock.in and it stopped with the  error   
>>>>> described as before.
>>>>>
>>>>> Thank you for your reply
>>>>> suxin
>>>>>
>>>>> On Jul 11, 2005, at 4:54 PM, Terry Lang wrote:
>>>>>
>>>>>
>>>>>
>>>>>> 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>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> =
>>>>>>>
>>>>>>> ----------------------------------------------------------------- 
>>>>>>> -- -- ---
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Dockdev mailing list
>>>>>>> Dockdev at docking.org
>>>>>>> http://blur.compbio.ucsf.edu/mailman/listinfo/dockdev
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> -- 
>>>>>> P. Therese Lang
>>>>>> Kuntz and James Labs
>>>>>> UCSF--Chemistry and Chemical Biology
>>>>>> Phone: (415)476-3986
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------- 
>>>>> -- -
>>>>> Suxin Zheng
>>>>> Research Associate
>>>>> Box 351700
>>>>> Department of Chemistry, University of Washington
>>>>> Seattle, WA, 98195-1700
>>>>> sxzheng at u.washington.edu
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> -- 
>>>> P. Therese Lang
>>>> Kuntz and James Labs
>>>> UCSF--Chemistry and Chemical Biology
>>>> Phone: (415)476-3986
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --------------------------------------------------------------------- -
>>> Suxin Zheng
>>> Research Associate
>>> Box 351700
>>> Department of Chemistry, University of Washington
>>> Seattle, WA, 98195-1700
>>> sxzheng at u.washington.edu
>>>
>>>
>>>
>>>
>>
>> -- 
>> P. Therese Lang
>> Kuntz and James Labs
>> UCSF--Chemistry and Chemical Biology
>> Phone: (415)476-3986
>>
>>
>>
>>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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