Re: [AMBER] Issue about "... . RESTARTED DUE TO LINMIN FAILURE..." (???)

From: David A Case <>
Date: Mon, 3 Aug 2020 10:16:16 -0400

On Mon, Aug 03, 2020, 辛志宏 wrote:

>I don't know fix the issue

> Small interatomic distances encountered:
> 54 49 4.54D-01

I don't think remote users can help very much here. The error message is very
clear, and the coordinates of atoms 49 and 54 are right there in your
input file:

atom 49: 34.31999 42.58892 38.77644
atom 54: 33.93647 42.57285 39.01973

How this happened is going to be something you will have to deal with
yourself. Is this the first step of a QM/MM calculation, or does it happen
during an MD or minimization calculation? You should certainly visualize the
coordinates you have (for the whole molecule) and see if something odd is
happening. Is atom 54 a link atom?

Can you make a simpler calculation (smaller QM region) that works? Or, try a
run with a semiempirical method like PM6, to see if you encounter any similar



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Received on Mon Aug 03 2020 - 07:30:03 PDT
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