[AMBER] mmpbsa.py

From: Urszula Uciechowska <urszula.uciechowska.biotech.ug.edu.pl>
Date: Thu, 9 Nov 2017 10:22:30 +0100

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)

My input for MMPBSA is:

startframe=1, endframe=1000, interval=1,
verbose=2, keep_files=0,
&pb inp=1, radiopt=0,

If i use as a input file:

startframe=1, endframe=1000, interval=1,
verbose=2, keep_files=0,

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.

Urszula Uciechowska PhD
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Abrahama 58
80-307 Gdańsk

Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego

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Received on Thu Nov 09 2017 - 01:30:02 PST
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