Re: [AMBER] atomiccorr: glibc detected *** cpptraj: malloc(): memory corruption:

From: Jason Swails <>
Date: Tue, 8 Jul 2014 15:05:14 -0700

On Tue, Jul 8, 2014 at 2:26 PM, Krisztina Feher <>

> Dear All,
> I used the atomiccorr function on a trajectory:
> trajin ../mut1_2w_dynV-100ns.netcdf netcdf
> atomiccorr .CA,C,N out aCorr_byRes.out cut 0.3 byres
> when I got this mesage:
> *** glibc detected *** cpptraj: malloc(): memory corruption:
> 0x0000000000e8f000 ***
> ^C
> I tried this on the raw trajectory including alll water, ions and on a
> imaged/centred trajectory without water and ions, it gave the same. I did
> not find anyone describing this error with cpptraj in the list archive. If
> anyone can help, it is very much appreciated.

​What version of cpptraj are you using? Does it pass all of the tests?
 There have been a number of bugs fixed, so make sure you are using
AmberTools 14 with all applied updates. If you are unsure whether all
updates have been applied, just reconfigure and recompile AmberTools 14.
 It will look for available updates and apply them if you allow it.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Jul 08 2014 - 15:30:02 PDT
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