Thanks Bill and Jason for suggestion.
Now it running fine, ptraj reading all trajectories for complex, ligand and
receptor after specifying them.
> 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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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Sun Sep 04 2011 - 00:30:02 PDT
