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

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 f

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

Does Autodocktools provide a command line for batch processing? G.V. On Thu, Jun 17, 2021 at 9:24 PM Saurabh Gayali wrote: > You should use autodocktools [ADT] or openbabel for this purpose. > Converting PDB to PDBQT. > > -- > > *Saurabh Gayali* / Post Doctoral Fello

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

You should use autodocktools [ADT] or openbabel for this purpose. Converting PDB to PDBQT. -- *Saurabh Gayali* / Post Doctoral Fellow saurabh.gay...@gmail.com / +91 8800412916 *CSIR-IGIB* New Delhi, India On Thu, Jun 17, 2021 at 4:01 PM Gundala

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

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? Sincerel