AMBER Archive (2008)

Subject: Re: AMBER: Nmode segmentation fault

From: David A. Case (
Date: Tue Mar 25 2008 - 11:34:37 CDT

On Tue, Mar 25, 2008, James Thomas wrote:
> I am running a nmode program using amber9 package. I tried using a smaller
> file as a test (the prmtop size: 566999 & the inpcrd: 50451). My interest
> protein has this (the prmtop size: 2307687 & the inpcrd size:210978).
> However, I got the error message of segmentation fault few minutes after I
> started the run.

It is much more helpful to know how many atoms you have in each case; the
size of the prmtop file itself is not very informative.
> My test run using test protein is successful to complete 100 steps of Newton
> minimization.

This sounds suspicious: Newton Raphson should generally converge in much less
than 100 steps. (You should have done a lot of CG minimization before
starting NR.)

> I also refer this :, but not
> sure on how to modify the alloc.f file.

This is about amber 6(!). Should be completely irrelevant for Amber 9.
> Is that because my protein of interest is too big?

See above...dac

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