Re: [AMBER] MMPBSA error

From: Ray Luo <rluo.uci.edu>
Date: Thu, 2 Jan 2020 16:37:15 -0800

Hi Rui,

I think you are probably using one of the earlier versions that set
radiopt=1 by default. Please set "radipot=0" after "istrng=0.150," in
your input file and you should be good to go.

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, Jan 2, 2020 at 4:29 PM Rui Chen <rchen6.ualberta.ca> wrote:
>
> Hello,
>
> I am running MMPBSA for the first time using the following script: (because
> I only want to check if the script works or not, so I specified large
> interval, so that I can get results in 5 min)
> Input file for running GB & PB
> &general
>    startframe=7000, endframe=7500, interval=100, keep_files=0,
> /
> &gb
>
>   igb=8,
>
>   saltcon=0.150, surften=0.0072,
>
>   surfoff=0.0, molsurf=0,
> /
> &pb
>   istrng=0.150,
> /
>
> I got the following error when I run PBSA and GBSA together: CalcError:
> /cm/shared/apps/amber16/bin/mmpbsa_py_energy failed with prmtop com.prmtop!
> PB Bomb in pb_aaradi(): No radius assigned for atom  6615  C1    Cg
>
> When I run GBSA alone, I got a different error:
> IOError: [Errno 2] No such file or directory:
> '_MMPBSA_complex_gb_surf.dat.0'
>
> How can I solve the problem? Looking forward to your reply.
>
> Best regards,
> Rui
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Received on Thu Jan 02 2020 - 17:00:02 PST