You want to use the triple trajectory approach, right? You only specified the complex trajectory with the -y flag. You will need to use the -yr and -yl flags to specify the receptor and ligand trajectories, respectively.
-Bill
On 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 &
>
>
>> 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 - 06:30:03 PDT
