[AMBER] Questions Regarding Structure Preparation and Protonation Errors for MD Simulation

From: ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER <amber.ambermd.org>
Date: Wed, 22 Apr 2026 11:50:09 +0000

Dear all,


I hope you are doing well.


I am currently preparing a system for molecular dynamics simulation as part of my thesis, and I would appreciate your guidance before proceeding further, as I encountered several issues that I am unsure how to properly handle.

The protein I am working on is 3POV. During the preparation, I followed these steps:

  1. I reconstructed missing chains using Chimera and selected the most suitable model based on steric considerations.

  2. I introduced a phosphorylated tyrosine residue at a specific position, as required for my thesis.

  3. I processed the structure using PDB4Amber to adjust naming conventions.

  4. I performed protonation using PDB2PQR (PROPKA, pH 7).

However, during the protonation step, I encountered several warnings and errors that I do not fully understand and am unsure whether they can be safely neglected.

In particular, the following issues were reported:

  * Missing atoms or failed protonation for multiple residues, including:

     * GLN 58

     * ARG 141

     * HIS 486

  * A structural issue where the histidine residue appears incomplete:

     * “His group does not seem to contain a ring”

  * Additional problems at the C-terminal and backbone regions:

     * SER 487 (BBN)

     * C-terminal residue (COO)

  * Warnings regarding magnesium ions not being recognized:

     * “Unable to find amino or nucleic acid definition for MG”

These messages suggest possible missing atoms or inconsistencies in the structure after chain reconstruction and modification.

At this stage, I am uncertain whether:

  * these issues can be ignored, or

  * the structure requires further correction before proceeding with topology generation and MD simulation.

I would greatly appreciate your advice on:

  * whether these errors are critical for continuing the workflow, and

  * the best approach to properly fix them, particularly in the context of modified residues such as phosphotyrosine.

Thank you very much for your time and support.


Kind regards,
Abdulrahman Walid




Abdulrahman Walid Attia Ibrahim ElBagoury
Antivirale und Antivirulenz-Wirkstoffe

Helmholtz-Institut für Pharmazeutische Forschung Saarland

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Received on Wed Apr 22 2026 - 05:00:03 PDT