[AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1?

From: He, Amy via AMBER <amber.ambermd.org>
Date: Mon, 5 Sep 2022 04:52:38 +0000

Dear Amber experts,

Iím using Amber/20, and I was simulating a protein-ligand complex. The ligand is noncovalent, and it has a bisulfite group (R-SO3) with a net charge of -1.

I wanted to experiment with the hydrogen mass partitioning method. So I prepared two prmtop files:

One is the original prmtop I generated by Leap. In the ATOMIC NUMBER section, the ligand sulfur atom is -1.
The other is the one I generated from the ParmED program in Amber with repartitioned masses. In the ATOMIC NUMBER section, the ligand sulfur atom is 16. That is the only difference I noticed except for the masses.

I tried both prmtop files for a minimization calculation. And I found that, with the ParmED prmtop file (which has 16 for the sulfer atom), the ligand structure appears to be distorted in the endpoint structure, and there is a 100x higher G Max at the final step.

Since the minimization with the original prmtop appeared to be normalÖ I tried to change 16 back to -1 in the ParmED generated, mass-repartitioned prmtop file. That seemed to solve my problem in minimization with hydrogen mass partitioning.

But I still donít understand what the cause was and why the ATOMIC NUMBER needs to be -1Ö What might be the problem? And why would I get a distorted ligand with the seemingly reasonable prmtop file (16 for Sulfur in ligand)? :í(

Thank you for your time and kind advice in advance. Please let me know if you need any further information.


Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
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Received on Sun Sep 04 2022 - 22:00:02 PDT
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