ADL: help virtual screening

Bagdevi bagdevi.mishra at gmail.com
Thu Jun 4 00:41:43 PDT 2009


you can always make a simple script to wrap another script of your
concern to deal with multiple files. I am attaching a perl script that
would take input a list of mol2 files and will convert them to pdbqt.

make a list of all mol2 files you have and name it as "mol2_list"
if you are on a linux machine, u can do this by the following command

ls *.mol2 >mol2_list

download the code attached to this mail, run it from the same
directory where your have all ur mol2 file and the list you just made.
In case you python codes are not in the executable path, you need to
give complete path of the code, or else copy the python code to ur
current directory.

Hope I could explain you, what I meant. In case of further doubt, feel
free to get back.

Regards,
Bagdevi Mishra.




On Thu, Jun 4, 2009 at 9:00 AM, venkat <vkabas at yahoo.com> wrote:
>
> Thanks Wim.
>
> But still waiting there is any potential way to do pdbqt files.
>
> i did able to split the mol2 by split command.
>
> Hoping there are some experts have all in one script file or some other easy way to do this !!!!!?
>
> Do you have that split_multi....py python script that you could send me,
>
> Thanks
> venkat
>
>
>
> ----- Original Message ----
> From: Wim Nerinckx <wimnerinckx at lavabit.com>
> To: autodock at scripps.edu
> Sent: Wednesday, June 3, 2009 6:47:04 PM
> Subject: Re: ADL: help virtual screening
>
> Hi Venkat,
>
> Here is a possibility:
>
> The AutoDock VS tutorial files contains the python script "split_multi_mol2_file.py" that is undocumented in the manual UsingAutoDock4forVirtualScreening_v4.pdf. You can use it with e.g.
>
> /split_multi_mol2_file.py -i yourmultimolfile.mol2
>
> That will split the "yourmultimolfile.mol2" into single mol2 files, one per molecule. Thereafter you can use the documented script for converting them all into pdbqt files.
>
> But I guess it is possible to do both together with a single script...
>
> WIM
>
> On 04 Jun 2009, at 00:36, venkat wrote:
>
>>
>> Hi all
>>
>> I would like to do virtual screening using autodock / vina.
>>
>> I do download the mol2 file from database, which has more than 1000, compounds.
>> Spliting all the file to single mol2 and do the pdbqt for docking really time consuming.
>> Is it any script or command line program that could generate pdbqs for all the mol2 file ?
>> Or let  me know is ther any efficient way to handle huge database without going through single
>> pdb for create the input (pdbqs) for docking.
>>
>> Really appreciate if any one could give some suggestions or any program they could able to share.
>>
>> thanks
>> venkat
>>
>>
>>
>> ________________________________________________
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>
>
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>
>
>
>
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