[Dock-fans] problem about the ranked result of DOCK6.2

[Scott Brozell]

Hi,

So dock6 terminated before all ligands were processed ?
If so then ligand_outfile_prefix_ranked.mol2 will be empty.
There can be no ranking of all the ligands before all the ligands
are processed.

#Flag to enable ranking by xx score over all ligands:
#the set of best scoring poses, one pose per ligand, will be sorted by
#xx score into descending order. The top poses will be written to
#file ligand_outfile_prefix_xx_ranked.mol2.

There may be something clever to do to micro-optimize the rerun,
but surely the simplest approach is just to rerun from scratch.

"Start small and scale up" to get the bugs out;
of course accidents do happen.

Good luck,
Scott


On Mon, 6 Apr 2009, CAI Qixu wrote:

> When I was docking with the functiong of "rank ligands", the process is
> break off by some reason, and at this time no result is in the
> ligand_outfile_prefix_ranked.mol2. Does it mean that I have to start from
> stratch??? Could any one help me to continue the docking process???
>
> On Sat, Apr 4, 2009 at 2:31 AM, Scott Brozell <sbrozell at rci.rutgers.edu>wrote:
>
>> Hi,
>>
>> So editing the file uses 1000, and copying to replace the file uses 2.
>> I wouldve guessed that both of those would have used 2.
>> Did you try removing the file and recreating it with 2 ?
>>
>> Scott
>>
>> On Wed, 1 Apr 2009, CAI Qixu wrote:
>>
>> I have make a test.
>>> First, after the DOCK6 is running in 1000-molecule inpput file, I edit the
>>> input mol2 file and delete the molecules to only 2 molecules left, and I
>>> found that the DOCK6 would not stop even the new mol2 file have finish.
>>> Second, after the DOCK6 is running in 1000-molecule input file, I use "cp"
>>> command to replace the 1000-molecule mol2 file with the new mol2 file
>>> which
>>> has only the top 2 molecules in old 1000-molecule mol2 file, and I found
>>> that the DOCK6 would stop after calculate 3 molecules. That is really very
>>> strange.
>>>
>>
>>  On Wed, Apr 1, 2009 at 2:19 AM, Scott Brozell <sbrozell at rci.rutgers.edu
>>>> wrote:
>>>
>>>  This may be operating system dependent as well as how you did the
>>>> replace (rm file followed by create file should use the original
>>>> 170000 file).  But in general, I'd expect most OS's and most other
>>>> ways of doing the replace to result in the 100000 file being used.
>>>>
>>>>  On Tue, 31 Mar 2009, CAI Qixu wrote:
>>>>
>>>>  I mean that when a ranked DOCK process(170000 molecules) is going, I
>>>>
>>>>> replace
>>>>> the input mol2 file(file 1)  with the other one mol2 file(file 2), which
>>>>> has
>>>>> less molecules in it(total 100000 molecules and they are the same as the
>>>>> .first 100000 molecules in the file 1). And I want to know what will
>>>>> happen?
>>>>> Thank you very much!
>>>>>
>>>>> On Tue, Mar 31, 2009 at 12:41 AM, Scott Brozell <
>>>>> sbrozell at rci.rutgers.edu
>>>>>
>>>>>> wrote:
>>>>>>
>>>>>
>>>>>  On Sun, 29 Mar 2009, CAI Qixu wrote:
>>>>>
>>>>>>
>>>>>> I have a serious problem. I screen a subset of small molecules in ZINC
>>>>>>
>>>>>> (about 170000 molecules), and I set the parameter "rank_ligands" to be
>>>>>>> "yes"
>>>>>>> and "max_ranked_ligands" to be "500"
>>>>>>> (1) Does it mean that in the process of docking, there is no output
>>>>>>> (because
>>>>>>> I find the ligand_outfile_prefix_ranked.mol2 is 0kb, and nothing is in
>>>>>>> the
>>>>>>> file after I have calculate 1000 molecules) ? And mol2 file and after
>>>>>>> all
>>>>>>> calculation finished, the final ranked mol2 file will generate, which
>>>>>>> have
>>>>>>> 500 ligands?
>>>>>>>
>>>>>>>
>>>>>>> Yes, ligand_outfile_prefix_ranked.mol2 will be empty until all ligands
>>>>>> have been processed, and yes it will ultimately contain 500 ligands.
>>>>>>
>>>>>> (2) When the DOCK is docking, I split the mol2 file of the ZINC subset
>>>>>> to
>>>>>>
>>>>>> two mol2 files, which contain 100000 molecules and 70000 molecules. And
>>>>>>> I
>>>>>>> overwrite the mol2(170000) with the mol2 file (100000) when the
>>>>>>> mol2(170000)
>>>>>>> is docking! I want to know whether  the docking process will stop at
>>>>>>> 170000
>>>>>>> molecules or 100000 molecules?
>>>>>>>
>>>>>>>
>>>>>>> Hmm, Im not sure i understand your question.
>>>>>> Apparently, you used the same ligand_outfile_prefix for all 3 runs ?
>>>>>> If so then there will be problems.
>>>>>>