ear Amber users,
While running mmpbsa.py (AMBER16) I am getting an error message:
PB Bomb in pb_aaradi(): No radius assigned for atom 2735 D1 DU
My complex contains Zn atom for which I used Cationic Dummy Atom (CaDA)
approach.
My input for MMPBSA is:
&general
startframe=1, endframe=1000, interval=1,
verbose=2, keep_files=0,
/
&pb
/
If i out the inp=1 and radiopt=0 in the pb section the error is:
/mmpbsa_py_energy': free(): invalid next size (normal): 0x0000000004fe7630
***
CalcError: /users/work/czarek/amber16/bin/mmpbsa_py_energy failed with
prmtop complex.top!
Error occured on rank 0.
Exiting. All files have been retained.
Is it possible to run mmpbsa.py (Amber 16) if I used CADA approach?
Any ideas how to fix the problem?
best
Urszula
--------------------------------------------
Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk
Poland
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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Received on Fri Nov 03 2017 - 00:30:02 PDT
