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

[CAI Qixu]

Hi,
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???
Thank you very much!!!
Qixu Cai
Email: caiqixu at gmail.com
Xiamen University, Fujian, China


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.
>>>>>
>>>>>
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