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

[Scott Brozell]

Hi,

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.

Scott

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.
>>