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 &
> 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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Received on Sat Sep 03 2011 - 06:30:02 PDT
