Try this command before running your mmpbsa.py
Source $AMBERHOME/amber.sh
or
Source $AMBERHOME/amber.csh
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Albert [mailto:mailmd2011.gmail.com]
Sent: Tuesday, January 31, 2017 1:31 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] MMPBSA failed
here is my settings:
&general
endframe=100, verbose=1,
/
&gb
igb=2, saltcon=0.150
/
&pb
istrng=0.150, fillratio=4.0
/
On 01/31/2017 08:28 AM, Albert wrote:
> Hello, I am trying to perform MM/PBSA with following command:
>
>
> mpirun -np 12 MMPBSA.py.MPI -O -i ../../infile/06-mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
> -lp lig.prmtop -y prod*.mdcrd
>
>
> But it constantly failed with the following messages:
>
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /soft/amber/16/bin/mmpbsa_py_energy
> cpptraj found! Using /soft/amber/16/bin/cpptraj Preparing trajectories
> for simulation...
> 100 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /soft/amber/16/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/soft/amber/16/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
> ",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
> ",
> line 476, in run
> self.prmtop))
> CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
> Error occured on rank 8.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8
> File "/soft/amber/16/bin/MMPBSA.py.MPI", line 100, in <module>
> app.run_mmpbsa()
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
> ",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/soft/amber/16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py
> ",
> line 476, in run
> self.prmtop))
> CalcError: /soft/amber/16/bin/cpptraj failed with prmtop com.prmtop!
> Error occured on rank 9.
> Exiting. All files have been retained.
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9
>
>
>
> I am just wondering where is the problem?
>
> Thank you very much.
>
> Albert
_______________________________________________
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
Received on Tue Jan 31 2017 - 01:30:03 PST
