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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Received on Tue Sep 27 2005 - 11:53:00 PDT
