Re: [AMBER] mmpbsa.py error

From: Ray Luo <rluo.uci.edu> Date: Fri, 3 Nov 2017 10:30:36 -0700

--
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 Fri, Nov 3, 2017 at 12:22 AM, Urszula Uciechowska
<urszula.uciechowska.biotech.ug.edu.pl> wrote:
>
> 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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