Hi,
This is interesting, I am not quite sure what is happening here and those
more experienced in ptraj can comment here. When you visualize
_MMPBSA_complex.mdcrd what does it look like? Try this option, in your
mmpbsa input file put netcdf=1 in the general section and see if you have
better luck.
On Tue, Jul 12, 2011 at 5:07 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Hi,
> In the _MMPBSA_ptraj1.out following is written:
>
> Setting box to be an exact truncated octahedron, angle is 109.471221
>
> PTRAJ: Processing input from file _MMPBSA_cenptraj.in
>
> PTRAJ: trajin 1.mdcrd 1 20 1
> Checking coordinates: 1.mdcrd
>
> gunzip: stdout: Broken pipe
> checkCoordinates(): Could not predict number of frames for AMBER trajectory
> file: 1.mdcrd
> If this is not a compressed file then there is a problem
>
> gunzip: stdout: Broken pipe
> Rank: 0 Atoms: 1092659 FrameSize: 26551647 TitleSize: 81 NumBox: 4 Seekable
> 0
>
>
> PTRAJ: trajin _MMPBSA_complex.mdcrd 1 20 1
> Checking coordinates: _MMPBSA_complex.mdcrd
> Could not process trajectory _MMPBSA_complex.mdcrd
>
> PTRAJ: trajin _MMPBSA_ligand.mdcrd 1 20 1
> Checking coordinates: _MMPBSA_ligand.mdcrd
> Could not process trajectory _MMPBSA_ligand.mdcrd
>
> PTRAJ: trajin _MMPBSA_receptor.mdcrd 1 20 1
> Checking coordinates: _MMPBSA_receptor.mdcrd
>
> At present I am only analyzing 1 ns of the production run for the GBSA
> calculation. I have compressed the .mdcrd file using gzip. But it seems
> that compressed .mdcrd is not read properly. I think this is creating the
> problem. There is any another way to slove the problem?
>
>
> mani
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>
--
T. Dwight McGee Jr.
Quantum Theory Project
University of Florida
Graduate Student
dwight.mcgee.gmail.com
"Problems cannot be solved at the same level of awareness that created
them."
Albert Einstein
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Received on Tue Jul 12 2011 - 19:00:02 PDT
