[AMBER] mmpbsa.py error

From: Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl>
Date: Fri, 3 Nov 2017 08:22:15 +0100

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
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