On Fri, Nov 21, 2025, Priyasha Majee via AMBER wrote:
>
>Kindly explain me this error and provide an elaborate explanation and
>fix.
>
>On 2025-11-20 19:35, Tomás Benjamín Cáceres Madariaga wrote:
>
>>Hi, this link contains relevant information about your issue.
>>http://archive.ambermd.org/202411/0053.html
Please see the link above, plus this one:
http://archive.ambermd.org/202411/0054.html
But the real reason behind this situation is that Amber's GB model expects
ion effects to be handled by the implicit solvent model, and not by
including explicit ions. I undestand that there are reasons why one might
want to have explicit ions, but be aware that you are in largely uncharted
territory here.
You might want to read this paper:
%A E.S. Kolesnikov
%A Y. Xiong
%A A.V. Onufriev
%T Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA
%J J. Chem. Theory Comput.
%V 20
%P 8724-8739
%D 2024
and also look at Section 4.2 in the Amber 2025 Reference Manual.
...regards...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 24 2025 - 07:30:02 PST
