Re: [AMBER] Minimization erro

From: David A Case <>
Date: Tue, 23 Jun 2020 21:02:05 -0400

On Tue, Jun 23, 2020, Renato Araujo wrote:
>I'm doing four minimization steps as follows:
>In the first, you specify the water and ion residues (cl- or Na +).
>In the second, only the protein residues (H minimization);
>In the third, it specifies protein + water (Leaving ions out).
>The last is a general minimization, I don't specify anything.
>The first three steps occur without errors, but the last one gives this
>messages in the terminal:

In addition to what Debarati DasGupta suggested, try running a (short)
serial job. But I'm guessing that you are seeing failures arising from
hydrogen atoms getting too close to other atoms, since you have very
large negative electrostatic energies.

The only safe way to run things is either to use SHAKE (which is what
most people do, if they are planning to use the minimization as a
starting point for subsequent MD); or use the "lmod" action in parmed to
get rid of hydrogens in zero vdW radii.

As an aside, if you *are* just minimizing to get ready for MD, you are
probably doing way more minimization (and more complex minimization)
than is necessary. Do just enough minimization to get rid of really bad
initial forces, then spend your computer time on MD, gradually releasing
the restraints.


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Received on Tue Jun 23 2020 - 18:30:02 PDT
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