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I am currently running a MD and I am calculating the energy from the trajectory using MMPBSA and it works normally, but now that I have to make a alanine scan I am following the documentation (https://ambermd.org/tutorials/advanced/tutorial3/py_script/index.htm) but as I errase the sidechain atoms manually to turn the residue of interest into an alanine and it shows tdiferent issues including "PrmtopError: Complex natom != receptor natom + ligand natom
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions."
But I don't really understand, because as it's a mutant it will never have the same amount of atoms
Can you help me?
Suggested improvement
No response
The text was updated successfully, but these errors were encountered:
Documentation Link
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Problem
Hello everyone
I am currently running a MD and I am calculating the energy from the trajectory using MMPBSA and it works normally, but now that I have to make a alanine scan I am following the documentation (https://ambermd.org/tutorials/advanced/tutorial3/py_script/index.htm) but as I errase the sidechain atoms manually to turn the residue of interest into an alanine and it shows tdiferent issues including "PrmtopError: Complex natom != receptor natom + ligand natom
Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions."
But I don't really understand, because as it's a mutant it will never have the same amount of atoms
Can you help me?
Suggested improvement
No response
The text was updated successfully, but these errors were encountered: