[AMBER] Segmentation error in minimization

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Mon, 28 Aug 2017 12:49:06 +0000

Dear Amber users

I am minimizing a glycosylated metalloprotein in 4 stages. Everything was fine for the first stage (all atoms except water and Na ions restrained) and the second stage (heavy atoms fixed). However, during the third minimization (only backbone atoms restrained) I get the error given below.

What I don't understand is that I've successfully run this same input before just using different parameters for the Zn site (the new ones should produce a more stable geometry). When superimposing the rst7 files of the two minimization3 runs there is almost no change in the Zn site or glycan positions. I noticed that at step 2700 the RMS is 5.8966E-02 and at step 2750 it is 6.2474E+05. The RMS values thereafter remain large until the run terminates with the error. Could this be triggering the crash? I've attached my min3.in, min3_error and min3.out files and would appreciate any suggestions on how to solve this.

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7FFFF636DBF7
#1 0x7FFFF636CDF0
#2 0x7FFFF565224F
#0 0x7FFFF636DBF7
#1 0x7FFFF636CDF0
#2 0x7FFFF565224F
#3 0x56C339 in nb_adjust_
#0 0x7FFFF636DBF7
#3 0x56C339 in nb_adjust_
#4 0x56E268 in ewald_force_
#4 0x56E268 in ewald_force_
#1 0x7FFFF636CDF0
#5 0x7AAF93 in force_
#5 0x7AAF93 in force_
#6 0x4E3712 in sander_
#6 0x4E3712 in sander_
#7 0x4D93A6 in MAIN__ at multisander.F90:?
#2 0x7FFFF565224F
#7 0x4D93A6 in MAIN__ at multisander.F90:?
#3 0x56C339 in nb_adjust_
#4 0x56E268 in ewald_force_
#5 0x7AAF93 in force_
#6 0x4E3712 in sander_
#7 0x4D93A6 in MAIN__ at multisander.F90:?
[cnode0846:74542] 2 more processes have sent help message help-mpi-runtime.txt / mpi_init:warn-fork
[cnode0846:74542] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Mon Aug 28 2017 - 06:00:11 PDT
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