Re: [AMBER] Na+ ion got stuck at one C-terminal end

From: Pengfei Li <>
Date: Fri, 26 Oct 2018 18:03:42 -0400

Hi Rakesh,

The interaction strength between the carboxylate group and Na+ ion can be strong. But you can check the Van der Waals and charge parameters of the Na+ ion to make sure you model the system correctly — you can use the “printDetails” command in ParmEd to do a quick check.

Hope it helps,

> On Oct 26, 2018, at 2:25 AM, Rakesh Srivastava <> wrote:
> Hello all,
> I am doing a simulation of a protein homo-dimer system and what I find is a
> Na+ ion has been stuck at one C-terminal end of one monomer for whole
> simulation length of 50ns. Should I worry and if yes then what might be
> possible solutions.
> Thanks in advance.
> Rakesh Srivastava
> Research Fellow
> School of Computational & Integrative Sciences
> Jawaharlal Nehru University, New Delhi-110067
> India
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Received on Fri Oct 26 2018 - 15:30:02 PDT
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