Dear Amber experts,
I’m 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 normal… 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 don’t understand what the cause was and why the ATOMIC NUMBER needs to be -1… What might be the problem? And why would I get a distorted ligand with the seemingly reasonable prmtop file (16 for Sulfur in ligand)? :’(
Thank you for your time and kind advice in advance. Please let me know if you need any further information.
Bests,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu
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Received on Sun Sep 04 2022 - 22:00:02 PDT
