Re: [PyMOL] Programmatically adding hydrogen and remove water to multiple PDB files

[sriram r. <hyp...@gm...>]

Hi Viswanath,
Please find the attach file which might help you,
You have to give the input folder path containing all the pdbs, for example
in terminal input:
"Please provide the input directory:/home/viswanath/pdb "and "Enter the
required files extension .pdb:.pdb" as input,
It will create a new folder "new" which will contain all the pdb files with
water removed and hydrogen added.
I hope that solves your issue.

Best wishes.
S.Sriram
Postdoctoral Research fellow,
Computational Structural Biology Team,
RIKEN Center for Computational Science(R-CCS), Kobe, Japan.

On Thu, Jun 17, 2021 at 6:16 PM Gundala Viswanath <gun...@gm...>
wrote:

> Does Autodocktools provide a command line for batch processing?
>
> G.V.
>
> On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali <sau...@gm...>
> wrote:
>
>> You should use autodocktools [ADT] or openbabel for this purpose.
>> Converting PDB to PDBQT.
>>
>> ------------------------------
>>
>> *Saurabh Gayali* / Post Doctoral Fellow
>> sau...@gm... / +91 8800412916
>>
>> *CSIR-IGIB*
>> <http://example.com/>New Delhi, India
>>
>>
>> On Thu, Jun 17, 2021 at 4:01 PM Gundala Viswanath <gun...@gm...>
>> wrote:
>>
>>> Hi
>>>
>>> I'm trying to dock a ligand to several hundred PDB files (receptors). I
>>> thus need to prepare those files like removing water and adding hydrogen.
>>>
>>> I can do that manually using Pymol. But it's too troublesome. Is there a
>>> way to do it programmatically with Pymol command line procedure?
>>>
>>>
>>> Sincerely,
>>>
>>> G.V.
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