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minghuilab / BindPPI

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Issue with pdb based prediction #2

Open chiragmathur27 opened 3 months ago

chiragmathur27 commented 3 months ago

Hi,

For a known complex 1Z92, i wanted to find the interactions usinng bindppi. I took the pdb from RSCB PDB. I am using the docker , so to run that i ran the command

docker run -v /home/ubuntu/BOLTPRO/Aswini/BindPPI/1Z92:/bindppi/1Z92 -it minghuilab/bindppi:v1 /bin/bash

then to predict, i ran the command, I have created the required files as well python BindPPI_RF13.py -i 1Z92

The error , it shows is At line 203 of file /home/lim9/softwares/charmm/psfres.F90 (unit = 1, file = 'fort.1') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE At line 203 of file /home/lim9/softwares/charmm/psfres.F90 (unit = 1, file = 'fort.1') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE At line 203 of file /home/lim9/softwares/charmm/psfres.F90 (unit = 90, file = 'fort.90') Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE Traceback (most recent call last): File "BindPPI_RF13.py", line 757, in <module> min_add_chain() File "BindPPI_RF13.py", line 322, in min_add_chain f = open(pathoutput+'/'+pdb_low+'_min.pdb','r') FileNotFoundError: [Errno 2] No such file or directory: '/bindppi/1Z92_out/1z92_min.pdb'

Could you please suggest, what should I do ?

Thanks

Liuyang9529 commented 3 months ago

Hello,

Thank you for bringing this to our attention. To align with the requirements of the CHARMM tool, kindly ensure that your working directory name is in all lowercase letters. Once you've made this correction and reattempted the operation, the issue you're experiencing should be resolved.

Best regards