Forget my last reply ;-) Marko is right, I didn't notice first because this is
fixed in PyMOL 2.1. Some PDBQT atom types were not imported correctly in
previous versions.
Cheers,
Thomas
> On Jul 26, 2018, at 10:21 AM, Marko Hyvonen wrote:
>
> Hi Baptiste,
>
> removing the data at the end
Hi Baptiste,
These files look good to me, I get:
PyMOL>rms Crystal_Rfp, Vina_Rfp
Executive: RMSD =0.032 (51 to 51 atoms)
Is it possible that you tried with a multi-model (multiple poses) pdbqt file
before? If that's the case, specify "mobile_state" and/or "target_state":
PyMOL>rms
Hi Baptiste,
removing the data at the end of the HETATM lines from ca.
character 70 onwards fixed it. Not sure what these are. According
to PDB 3.30 format, 67-76 should be empty. Some of the elements
were non-standard also (NA for N, OA for O), but looks
Thanks for your answers. The molecule is the rifampicin. Please find
attached the pdb from the crystal structure and the pdbqt from autodock
vina. May be the format of one or both files is not correct.
Best,
Baptiste
Le 25/07/2018 à 18:57, Markus Heller a écrit :
Not knowing what your
Not knowing what your molecule looks like, could it be automorphism?
> -Original Message-
> From: Baptiste Legrand
> Sent: Wednesday, July 25, 2018 9:17 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Calculate RMSD between ligands from a crystal structure and
> from a