Hi I was going through tutorial but they have also used same script with y*.crd
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm
[
http://ambermd.org/tutorials/advanced/tutorial3/images/ras-raf2.jpg]<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm>
Amber Advanced Tutorials - Tutorial 3 - MMPBSA.py - Section 1<
http://ambermd.org/tutorials/advanced/tutorial3/py_script/section1.htm>
ambermd.org
This tutorial explains how to carry out MM-PBSA simulations using AMBER - Section 1
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Friday, July 8, 2016 7:07:46 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA
Please check the "MMPBSA.py --help" and amber manual.
> mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o
FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp
receptor.prmtop -lp peptide.prmtop -y *.crd
You clearly specified " -y *.crd" in your command.
Make sure to understand every command you are using.
Hai
On Fri, Jul 8, 2016 at 2:02 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi Nahi
> No I don't have any file with such extension
>
> Sent using OWA for iPhone
> ________________________________
> From: Nhai <nhai.qn.gmail.com>
> Sent: Friday, July 8, 2016 6:03:40 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA
>
> Do you have any filename with .crd extension in your folder?
>
> Hai Nguyen
>
> > On Jul 8, 2016, at 12:57 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> >
> > Hi
> >
> > I am trying to do MMPBSA calculation using script
> >
> >
> > mpirun -np 4 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.out -sp PRMT7_WT_NH1.prmtop -cp complex.prmtop -rp
> receptor.prmtop -lp peptide.prmtop -y *.crd
> >
> >
> >
> > But I am getting an error which I am unable to solve it
> >
> >
> > Error: *.crd matches no files.
> > File "/nethome/axt651/apps/amber14/bin/MMPBSA.py.MPI", line 103, in
> <module>
> > app.file_setup()
> > File
> "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 156, in file_setup
> > self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > File
> "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 59, in make_trajectories
> > traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > File
> "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 467, in __init__
> > self.Query()
> > File
> "/nethome/axt651/apps/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 602, in Query
> > raise TrajError('%s failed when querying %s' % (self.exe, traj))
> > TrajError: /nethome/axt651/apps/amber14/bin/cpptraj failed when querying
> *.crd
> > Error occured on rank 0.
> > Exiting. All files have been retained.
> >
> --------------------------------------------------------------------------
> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 1.
> >
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> >
> >
> > I have cross checked MMPBSA.py.MPI is correctly installed in amber home
> directory
> > Kindly help me out.
> >
> >
> > thanking you,
> > -AT
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
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Received on Fri Jul 08 2016 - 12:00:03 PDT
