Dear amber.
I was doing MD using amber on protein ligand interaction with MMPBSA, the Fe atom is not recognized by MMPBSA when doing decomposition.
I have re-installed amber and add the modified mdread.f in the attachment. But the errors are also as follows
Beginning GB calculations with sander...
calculating complex contribution...
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
bad atom type: FE
bad atom type: FE
bad atom type: FE
bad atom type: FE
Error: sander error during GB calculations!Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Exit code -5 signaled from bnode12
Killing remote processes...MPI process terminated unexpectedly
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
bad atom type: FE
Error: sander error during GB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py --clean to erase these files.
Is there a solution to solve this?
best regards
372133720
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- application/octet-stream attachment: mdread.f
Received on Tue Jul 30 2013 - 04:00:02 PDT
