We are facing an segmentation error with two different class of proteins at minimization step in amber. A DNA-gyrase B protein and an ecto-nucleotidase. Both the PDB's are with optimal resolution. We found no error during topology and coordination file preparation in both cases. Minimization parameters were also simple as shown in tutorial for 2000 step without any restrain.?
Segmentation fault, exit code:139
The error is as shown below screenshot. Need help
Thank you in advance
Hi Jaya,
Check that the topology of your molecule is correct, that usually appears when there are errors in the structure of you receptor or ligand, for example that your receiver has missing parts or some bonds are not well described in the file.prmtop.
Hi Jaya,
Firstly, you should check that the following lines are included in your .bashrc.
export AMBERHOME=/installing/path/amber1x
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
source $AMBERHOME/amber.sh
If this is OK, then you should reboot the computer.
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