> So do you see any error message in the sander output when running with
> the first input, which is recommended?
Yes after 50minutes of calculations the error is:
amber16/bin/sander failed with prmtop complex.top!
>
> When you use the second input, you implicitly used radiopt=1, which
> asks the program to assign radii for all atoms. However it apparently
> doesn't know anything about D1/DU, so you saw the error message.
After using second input: the error message is: PB Bomb in pb_aaradi(): No
radius assigned for
atom
2735 D1 DU
How can I fix this problem, in previous versions AMBER10 and 11 I did not
have this error while running mmpbsa.
best
Urszula
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical Physics, Biomedical Engineering, and Chemical Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
>
> On Thu, Nov 9, 2017 at 1:22 AM, Urszula Uciechowska
> <urszula.uciechowska.biotech.ug.edu.pl> wrote:
>>
>> 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/
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--------------------------------------------
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/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 09 2017 - 07:30:02 PST
