In order to prepare a receptor file for docking, we need to remove the ligand associated with the protein; as in the pdb files from Protein Data Bank, coordinates for ligand is also mentioned. So, how to remove the ligand?
Use chimera. Select-residues-ligand. It will automatically get highlighted.
Use chimera. Select-residues-ligand. It will automatically get highlighted.
Maninee Shrivastava
you can use Biovia discovery studio open your PDB and just click on the ligand and delete it.
if you want to know the coordinate of ligand just right click on the ligand and click on the attribute.
best luck.
Hello
You can use pymol by clicking "S" at the bottom, in the pymol viewer select the ligand, the ligand will be highlight with different color then right click on it and choose remove. The ligand will automatically remove from the protein.
No need for a molecular graphics program: PDB files are plain text files . . . and those from the Protein Data Bank contain a lot of very useful information besides the atomic coordinates.
you can use many tools such as chimera, pymol, autodock tools.
when using pymol, select the ligand from the sequence and then delete it.
when using autodock tool.
select--> select from string-> click residue sets-->choose the ligand-->click add--> go to edit--->delete selected atoms then your done.
discovery studio visualizer DSV is the easiest way for that
first open DSV, select ligand then delete it
I wrote this script if it can help:
https://github.com/lucagl/MOAD_ligandFinder
However, in the current version you will obtain a pqr file without the ligand whilst the original pdb file remains untouched..
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