Hi, Anthony
ptraj uses normal file operating interface which doesn't support file
more than 2 GB on a 32-bit system.
Here is some suggestion for you problem:
1. use gzip to compress the trajectory file, and specify the
compressed file instead of the original file in trajin command.
So that ptraj will call gunzip to decompress the file, which
may support large file big than 2GB(I am not sure). (If you are
using a linux system, your glibc version must be higher than 2.2.0,
and you linux kernel must be higher than 2.4.0
2. If this doesn't work, I suggest you to find a 64-bit machine
running a 64-bit operating system. and try ptraj on it.
Meanwhile, I will work on the code of ptraj to see if I can enable Large
File Support on it.
Sincerely,
Wei Zhang
On Thu, 2005-09-22 at 14:24 -0600, Anthony Cruz wrote:
> Hi Users:
> I trying to do an rms analysis and I found this problem:
> ptraj spc_T.atop < rms.in > measure_rmsd.out
> Read in control variables
> Read in atom names...
> Read in charges...
> Read in masses...
> Read in IAC (atoms involved in L-J)...
> Read in NUMEX (index to excl atom list)...
> Read in NNO (index for nonbond of .type)...
> Read in residue labels...
> Read in the residue to atom pointer list...
> Read in bond parameters RK and REQ...
> Read in angle parameters TK and TEQ...
> Read in dihedral parameters PK, PN and PHASE...
> Read in SOLTY...
> Read in L-J parameters CN1 and CN2...
> Read in info for bonds w/ hydrogen...
> Read in info for bonds w/out hydrogen...
> Read in info for angles w/ hydrogen...
> Read in info for angles w/out hydrogen...
> Read in info for dihedrals w/ hydrogen...
> Read in info for dihedrals w/out hydrogen...
> Read in excluded atom list...
> Read in h-bond parameters: AG, BG, and HBCUT...
> Read in atomic symbols (types)...
> Read in tree information...
> Read in the JOIN info...
> Read in the IROTAT info...
> Checking coordinates: foorem_REP.mdcrd.000
>
> ERROR in readAmberTrajectory(): Set #386336 is corrupted (
> l�?�?W?��7)...
>
> When I try to truncate the trajectory at 386335 I found this:
>
> ptraj spc_T.atop < trunc.in
>
> Amber8 Module: ptraj
>
> Read in control variables
> Read in atom names...
> Read in charges...
> Read in masses...
> Read in IAC (atoms involved in L-J)...
> Read in NUMEX (index to excl atom list)...
> Read in NNO (index for nonbond of .type)...
> Read in residue labels...
> LEU ILE PRO CYS CYS PRO VAL ASN LEU
> LYS ARG VAL VAL VAL LEU LEU GLY ALA
> VAL LEU VAL VAL ILE VAL GLY ALA
> LEU LEU MET GLY LEU
> Read in the residue to atom pointer list...
> Read in bond parameters RK and REQ...
> Read in angle parameters TK and TEQ...
> Read in dihedral parameters PK, PN and PHASE...
> Read in SOLTY...
> Read in L-J parameters CN1 and CN2...
> Read in info for bonds w/ hydrogen...
> Read in info for bonds w/out hydrogen...
> Read in info for angles w/ hydrogen...
> Read in info for angles w/out hydrogen...
> Read in info for dihedrals w/ hydrogen...
> Read in info for dihedrals w/out hydrogen...
> Read in excluded atom list...
> Read in h-bond parameters: AG, BG, and HBCUT...
> Read in atomic symbols (types)...
> Read in tree information...
> Read in the JOIN info...
> Read in the IROTAT info...
> Successfully completed readParm.
> PTRAJ: Processing input file...
> Input is from standard input
>
> PTRAJ: trajin foorem_REP.mdcrd.000 1 386335
> Checking coordinates: foorem_REP.mdcrd.000
>
> PTRAJ: trajout foorem_REP.mdcrdc.000
>
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 386335 frames.
> Summary of I/O and actions follows:
>
> INPUT COORDINATE FILES
> File (foorem_REP.mdcrd.000) is an AMBER trajectory with 386335 sets
>
> OUTPUT COORDINATE FILE
> File (foorem_REP.mdcrdc.000) is an AMBER trajectory (with box info)
>
> ACTIONS
> Stack is NULL
>
> Processing AMBER trajectory file foorem_REP.mdcrd.000
>
> Set 1 .................................................
> Set 50 .................................................
> Set 100 .................................................
> Set 150 .................................................
> Set 200 .................................................
> Set 250 .................................................
> Set 300 .................................................
> Set 350 .................................................
> Set 400 .................................................
> .
> .
> .
>
> Set 152750 .................................................
> Set 152800 .................................................
> Set 152850 .................................................
> Set 152900 .................................................
> Set 152950 .................................................
> Set 153000 .................................................
> Set 153050 .................................................
> Set 153100 .................................................
> Set 153150 .File size limit exceeded
>
>
> Why the error about the file size??? the original file have 5G..
>
> Anthony
>
>
>
>
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--
Wei Zhang <zweig.scripps.edu>
The Scripps Research Institute
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Received on Tue Sep 27 2005 - 17:53:01 PDT
