Re: [AMBER] Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

From: David A Case <>
Date: Sun, 6 Jun 2021 08:18:44 -0400

On Sun, Jun 06, 2021, Akinyemi Omoniyi wrote:

>I have checked the min2.out file and the thing that I noticed was that the
>file is incomplete when compared with the similar file from the tutorial.

You have a very bad bond energy, so something must have gone wrong during
the setup phase:

       1 -2.9452E+05 2.8379E+01 9.2002E+03 SG 6627

  BOND = 1097341.6452 ANGLE = 5491.1031 DIHED = 2344.1542
  VDWAALS = 213685.2572 EEL = -1644142.2256 HBOND = 0.0000
  1-4 VDW = 2813.7314 1-4 EEL = 27269.5779 RESTRAINT = 0.0000
  CMAP = 679.8318

Use the checkstructure action in cpptraj to look for bad bonds, and see if
that helps to pinpoint the problem. You might also visualize your system
with VMD or Chimera to see if you can pinpoint what is wrong.

This looks like a very large system(?) If you are new to Amber, you might
want to try smaller calculations first to gain experience about what to

...good luck...dac

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Received on Sun Jun 06 2021 - 05:30:03 PDT
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