Re: [AMBER] Energy minimization problem

From: David A Case <>
Date: Sun, 14 Mar 2021 08:56:48 -0400

On Sun, Mar 14, 2021, richa anand wrote:
>I am trying to simulate protein_mrna_sirna complex. I tried to run energy
>minimization (using Sander (serial) Amber20) with the input file:

Things to check:

What does the initial energy look like? Is there a large VDW component that
would indicate bad contacts? It's also worth running the "checkstructure"
action in cpptraj on the initial structure.

Have you tried setting ntr=1 and restraining the solute molecules to their
initial positions?

Have you set iwrap=1? If so, return it to its default value of 0.

Notes: 10 is very small for a buffer in the solvatebox command, but it
seems unlikely to cause what you see. Also, if you are preparing for MD,
you should only need about 1000 steps of minimization. See the protocol
descibed here:

%A D.R. Roe
%A B.R. Brooks
%T A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations
%J J. Chem. Phys.
%V 153
%P 054123
%D 2020


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Received on Sun Mar 14 2021 - 06:00:03 PDT
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