Differences between `*_rigid.pdbqt` and `*.pdbqt` files of receptors

[eunos-1128]

Hi,

I prepared *_rigid.pdbqt and _*_flex.pdbqt files using prepare_flexreceptor.py for flexible docking with vina scoring function.

Beforehand, I executed ordinary dockings (only receptors rigid) and on that time I prepared usual *.pdbqt files of receptors using the ADFRsuite script.

I'm not sure of differences between usual *.pdbqt and *_rigid.pdbqt files.

Can I use *.pdbqt files for flexible docking instead of using *_rigid.pdbqt if they are regarded as actually same ones(because *.pdbqt files are supposed to be rigid)?

if *_rigid.pdbqt files have differences from *.pdbqt ones, I'd like to know what is different from.

Regards,

[rwxayheee]

hi @eunos-1128 The two files are different. The PDBQT with “rigid” in its name doesn’t contain the sidechain of the modified residue. If you use a file comparison tool you can get a better look how they differ.

For grid map computing (autogrid) and for docking, it makes more sense to use the “rigid” PDBQT as the receptor. Doing this excludes the sidechain from being doubly counted in receptor and flexible residue (which is essentially part of the mobile “ligand” in flexible docking)

[eunos-1128]

@rwxayheee

Thank you! I understand :)