Re: [AMBER] Segmentation error in minimization

From: David A Case <>
Date: Mon, 28 Aug 2017 11:03:23 -0400

On Mon, Aug 28, 2017, Lizelle Lubbe wrote:
> I am minimizing a glycosylated metalloprotein in 4 stages. Everything
> was fine for the first stage (all atoms except water and Na ions
> restrained) and the second stage (heavy atoms fixed). However, during
> the third minimization (only backbone atoms restrained) I get the error
> given below.
> What I don't understand is that I've successfully run this same input
> before just using different parameters for the Zn site (the new ones
> should produce a more stable geometry). When superimposing the rst7
> files of the two minimization3 runs there is almost no change in the
> Zn site or glycan positions. I noticed that at step 2700 the RMS is
> 5.8966E-02 and at step 2750 it is 6.2474E+05. The RMS values thereafter
> remain large until the run terminates with the error. Could this be
> triggering the crash? I've attached my, min3_error and min3.out
> files and would appreciate any suggestions on how to solve this.

At around step 2750 the 1-4EEL energy becomes nonsensical. I'm guessing
that you have a hydrogen atom (or something else with a zero-vdW radius)
that is coming very close to a zinc atom. Look around atom 6143 in your
structure, and see if it could be doing something bad.

....good luck....dac

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Received on Mon Aug 28 2017 - 08:30:02 PDT
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