Date: Mon, 30 Mar 2026 18:01:44 +0000
Thank you for clarifying this and I will try it as well. I also appreciate both the video and your article with the quick tips.
Finally, regarding the usage of the Modeller part, should I perform this step prior to the docking and MD simulation protocols that I previously provided?
Also, concerning my previous protocol, are the steps in the correct order, and would it be appropriate to proceed with this workflow, or would you recommend any modifications?
Best Regards,
Abdulrahman
Abdulrahman Walid Attia Ibrahim ElBagoury
Antivirale und Antivirulenz-Wirkstoffe
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From: Téletchéa Stéphane via AMBER <amber.ambermd.org>
Sent: Monday, March 30, 2026 7:04 PM
To: amber.ambermd.org
Subject: Re: [AMBER] [EXTERN] Re: Ligand Prepartion
Le 30/03/2026 à 17:02, ElBagoury, Abdulrahman Walid Attia Ibrahim via
AMBER a écrit :
> At this step, I encounter an error indicating a backbone gap between CYS A 314 and ARG A 319, and pdb2pqr stops because the biomolecular structure is incomplete. However, when I run pdb2pqr on the original PDB file (before docking/export from MOE), the protonation runs without any errors.
Dear all,
This is a classical error with PDB files with missing residues, which is
very often with PDB files,
for many reasons, one being for instance the lack of experimental support.
It is not an issue when you docking only, since most of the time the
protein is kept rigid,
and probably the residues involved in the binding are not those of the
missing part.
You should complete your pdb file using MODELLER for instance, you can
do it in Chimera:
https://rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-modeling.html
I found also videos of this (not mines) if that helps:
- https://www.youtube.com/watch?v=GV6jHhxR5T4
- (and many others).
This should not change a lot the conformation and/or the binding site (I
assume not),
but will solve the problem for AMBER modelling.
To be complete, we set up a series of "quick tips" last year, to help
people getting
through these problems and questions more easily:
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013030
We'll submit another article this year covering more specifically the
problem you are facing,
as it is quite common and a bit disturbing while being alone to find a
solution.
HTH,
Stéphane
-- Maître de conférences Hors Classe, PEDR, HDR US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics, F-44000 Nantes http://www.us2b.univ-nantes.fr/ - http://www.steletch.org _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber
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