Gabriela Lima
Hello, I'm trying to run gmx_MMPBSA on the university cluster.
The following error is occurring:
[INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [DEBUG ] Running command: echo -e "name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /opt/spack/opt/spack/linux-centos7-x86_64_v3/gcc-12.2.0/gromacs-2023-iowv3qlngbq56ofmnexzucmfjjtducq2/bin/gmx_mpi make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f 6_md.tpr [DEBUG ] [n07:159520] *** Process received signal *** [DEBUG ] [n07:159520] Signal: Segmentation fault (11) [DEBUG ] [n07:159520] Signal code: Invalid permissions (2) [DEBUG ] [n07:159520] Failing at address: 0x2b2470a4b648 [DEBUG ] [n07:159520] [ 0] /usr/lib64/libpthread.so.0(+0xf630)[0x2b24711c0630] [DEBUG ] [n07:159520] [ 1] /opt/spack/opt/spack/linux-centos7-x86_64_v3/gcc-12.2.0/gromacs-2023-iowv3qlngbq56ofmnexzucmfjjtducq2/bin/../lib64/libgromacs_mpi.so.8(debug+0x0)[0x2b2470a4b648] [DEBUG ] [n07:159520] *** End of error message *** [ERROR ] MMPBSA_Error
/opt/spack/opt/spack/linux-centos7-x86_64_v3/gcc-12.2.0/gromacs-2023-iowv3qlngbq56ofmnexzucmfjjtducq2/bin/gmx_mpi make_ndx failed when querying index.ndx
The log, slurm and input files are attached.
gromacs version: 2023
gmx_MMPBSA version: gmx_MMPBSA v1.6.1+8.gb4186d8 based on MMPBSA version 16.0 and AmberTools 20
Thank you!
