AMBER Archive (2008)

Subject: AMBER: measuring contacts: error "glibc detected"

From: rebeca_at_mmb.pcb.ub.es
Date: Fri Mar 28 2008 - 07:26:42 CDT

Hello,
I am trying to measure the contacts in the unfolding of a protein, using the
ptraj module of amber 9.0 and the option "contacts".

My input is this one:

trajin ../trajectory/traj_500ns_nobox_500.crd
contacts first byresidue out contacts_out @CA
go

It seems that the program reads the 500 frames of the trajectory, but then it
stops:

Processing AMBER trajectory file ../trajectory/traj_500ns_nobox_500.crd

Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 .................................................
Set 450 .................................................
Set 500

In the error file, I can see:

Residue labels:

  Checking coordinates: ../trajectory/traj_500ns_nobox_500.crd
*** glibc detected *** double free or corruption (out): 0x0000000010105270 ***
srun: error: s04c4b03: task0: Segmentation fault
srun: Terminating job

I have seen this error in the forum, but it was unresolved, or at least, I could
not find the answer. Please, could anyone experience a similar problem or has
any idea of the solution?

Thank you very much for your help in advance,

Rebeca García Fandiño
Parc Cientific de Barcelona
regafan_at_usc.es

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu