Re: [AMBER] MMPBSA.py is crashing

From: manikanthan bhavaraju <manikanthanbhavaraju.gmail.com>
Date: Tue, 12 Jul 2011 16:07:26 -0500

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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Received on Tue Jul 12 2011 - 14:30:03 PDT
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