On Sat, Sep 3, 2011 at 9:08 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
> Thanks for reply
>
> But I have already checked total number of atom in complex is equal to sum
> of
> atoms in receptor and ligand.
> 825+1011=1836
>
> command line I am using:
> mpirun -np 8 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
> 1ig7-strip.prmtop -rp TG-strip.prmtop -lp Q50-strip.prmtop -y *.mdcrd >
> progress.log &
>
I think I know what happened here. MMPBSA.py thinks every .mdcrd file in
your directory is a complex trajectory file, and i'm guessing your receptor
and ligand trajectory files are included here. You have to tell MMPBSA
which trajectories belong to the receptor (with the -yr flag like Bill said)
and which trajectories belong to the ligand (with the -yl flag like Bill
said as well).
HTH,
Jason
>
> > It appears as if there is a discrepancy between the atoms in your or
> prmtop
> > files and your trajectory files. Double check that these are compatible.
> Also,
> > if you still can't find the problem can you post the command line
> argument you
> > supplied to run this calculation?
> >
> > -Bill
> >
> >
> >
> > On Sep 3, 2011, at 8:00 AM, "Sangita Kachhap" <sangita.imtech.res.in>
> wrote:
> >
> >>
> >> Hello all
> >> I am attempting to run MMPBSA by triple trajectory approach.
> >> I have three seperate trajectory for complex, receptor and ligand.
> >> When I am using these trajectory to run MMPBSA.py, ptraj is not able to
> >> read frame in receprtor and ligand, reading only complex trajectory
> frame.
> >>
> >> I am not getting where is the fualt?
> >>
> >>
> >> Here is my script:
> >>
> >> input file for running GB
> >>
> >> &general
> >> startframe=1, endframe=400, verbose=1, strip_mdcrd=0,
> >> /
> >> &gb
> >> igb=2, saltcon=0.100
> >> /
> >>
> >>
> >> Here is the ptraj.out file
> >>
> >> PTRAJ: Processing input from file _MMPBSA_cenptraj.in
> >>
> >> PTRAJ: trajin Q50-NPT_strip.mdcrd 1 400 1
> >> Checking coordinates: Q50-NPT_strip.mdcrd
> >> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory
> >> file: Q50-NPT_strip.mdcrd
> >> If this is not a compressed file then there is a problem
> >> Rank: 0 Atoms: 1836 FrameSize: 44615 TitleSize: 30 NumBox: 0 Seekable 0
> >>
> >>
> >> PTRAJ: trajin Q50-TG_NPT-strip-400ps.mdcrd 1 400 1
> >> Checking coordinates: Q50-TG_NPT-strip-400ps.mdcrd
> >> Rank: 0 Atoms: 1836 FrameSize: 44640 TitleSize: 30 NumBox: 3 Seekable 1
> >>
> >>
> >> PTRAJ: trajin TG-NPT_strip.mdcrd 1 400 1
> >> Checking coordinates: TG-NPT_strip.mdcrd
> >> checkCoordinates(): Could not predict number of frames for AMBER
> trajectory
> >> file: TG-NPT_strip.mdcrd
> >> If this is not a compressed file then there is a problem
> >> Rank: 0 Atoms: 1836 FrameSize: 44615 TitleSize: 30 NumBox: 0 Seekable 0
> >>
> >>
> >>
> >> Can anyone please
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Sep 03 2011 - 08:30:03 PDT
