[AMBER] Troubleshooting SHAKE problems in minimization

From: Alen Ahmetovic <alen2.mail.usf.edu>
Date: Sun, 27 May 2018 00:07:29 -0400

As the title suggests I'm running into problems with getting complexes
through minimization. Below is the minimization input I am using:

minimise complex_sol

If I change ntc=1 the minimization will run through the first 500 steps,
and fail on the second. During the second 500 steps, I keep running into
segmentation faults, specifically error:11, if that means anything. I have
absolutely no coding experience so when I try to troubleshoot online the
tips are way over my head. I've tried this on two separate computers and
keep getting the same segmentation fault. I tried to use cpptraj but since
minimization restricts the complex, there is no trajectory file to input to
view to check for atom overlaps, etc.

I've also tried messing with the maxcyc (ncyc), changing ntpr to smaller
values to see exactly where it fails (usually a few steps into the second
cycle of the minimization).

Any tips or ideas on how to analyze where the problem might be occurring
(like cpptraj) would be greatly appreciated. If there is more information
specific to how I made the structures or the specific errors I'm getting
that I should post as well, please let me know. I've looked through these
forums and it seems just about everyone is getting SHAKE problems after
minimization, not before, so I'm not sure where else to look.

Thanks all.
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Received on Sat May 26 2018 - 21:30:02 PDT
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