[AMBER] mdread MMPBSA

From: tianchuan1015 <tianchuan1015.gmail.com>
Date: Tue, 30 Jul 2013 18:19:27 +0800

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
tianchuan1015

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Received on Tue Jul 30 2013 - 03:30:03 PDT
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