Dear Ray,
I changed the input file to:
Input file for running GB & PB
&general
startframe=7000, endframe=7500, interval=100, keep_files=0,
/
&gb
igb=8,
saltcon=0.150, *radipot=0,* surften=0.0072,
surfoff=0.0, molsurf=0,
/
&pb
istrng=0.150, *radipot=0,*
/
I got the following error:
InputError: Unknown variable radipot in &gb
Enter `MMPBSA.py.MPI --help` for help
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status,
thus causing
the job to be terminated. The first process to do so was:
Process name: [[31708,1],0]
Exit code: 1
By the way, I used Amber/16 (the newest version) in our local cluster to
calculate the binding free energy. Should I use other clusters and maybe
the newest version of Amber?
Best regards,
Rui
On Thu, Jan 2, 2020 at 5:38 PM Ray Luo <rluo.uci.edu> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 02 2020 - 22:00:02 PST
