[gmx-users] can't generate pdb file in g_cluster

Nizar Masbukhin nizar.fkub08 at gmail.com
Thu Jan 1 10:41:06 CET 2015

hi gromacs users,

while i was trying to cluster structure using:

 g_cluster_mpi -f traj -s chainB.pdb -method gromos -cl out.pdb -n

error message appeared

[nizars-mbp:01757] *** Process received signal ***

[nizars-mbp:01757] Signal: Segmentation fault: 11 (11)

[nizars-mbp:01757] Signal code: Address not mapped (1)

[nizars-mbp:01757] Failing at address: 0x0

[nizars-mbp:01757] [ 0] 0   libsystem_platform.dylib
0x00007fff924485aa _sigtramp + 26

[nizars-mbp:01757] [ 1] 0   ???
0x0000206000000000 0x0 + 35596688949248

[nizars-mbp:01757] *** End of error message ***

this wasn't happening if i am not using -cl flag.

what is libsystem_platform.dylib ?
do i miss some library?
My Best Regards, Nizar

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