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

[Scott Brozell]

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.
>>>>