Dear Amber users,
While running mmpbsa.py (AMBER16) I am getting an error message after 50
min of calculations that
amber16/bin/sander failed with prmtop complex.top!
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 inp=1, radiopt=0,
/
If i use as a input file:
&general
startframe=1, endframe=1000, interval=1,
verbose=2, keep_files=0,
/
&pb
/
The error message is: PB Bomb in pb_aaradi(): No radius assigned for atom
2735 D1 DU
I went through the previous user lists messages, but there is no clear
answers that I could find.
Thanks in advance for any help.
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 Thu Nov 09 2017 - 01:30:02 PST
