Just a thought.
>> PTRAJ: trajin 1.mdcrd 1 20 1
>> Checking coordinates: 1.mdcrd
>>
>> gunzip: stdout: Broken pipe
If you really gzipped the mdcrd file, then they usually have a .gz
ending as filename
e.g. If I do gzip 1.mdcrd I would get 1.mdcrd.gz
then, when trajin tries to read '1.mdcrd' it would not find it.
Try NOT gzipping it first and see what happens.
On 7/13/11 3:35 AM, Dwight McGee wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
--
Dr. Adrian E. Roitberg
Full Professor
Quantum Theory Project, Department of Chemistry
University of Florida
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Wed Jul 13 2011 - 00:00:03 PDT
