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 suggest me where I am doing wrong?
>
> With regards
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
>
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Received on Sat Sep 03 2011 - 05:30:04 PDT
