AMBER Archive (2005)

Subject: Re: AMBER: REMD error!!!

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 20 2005 - 07:05:41 CDT


1) check your restart file

spcrem_REP.rst.006 visually (using vi or a text editor).

does it look ok? any corrupted lines, or ***, or something else
wrong? Can you load that coordinate file into a program like VMD?

2) the command for ptraj is trajout, not trjout. Fix that and rerun it.

Anthony Cruz wrote:

>Hi User:
>
>I was doing a Replica exchange dynamics simulation of a small peptide with 16
>temperature. The simulation stop before it ends. I have the following
>information from PBS:
>
>***************
>logfile (*.log)
>***************
> RUNNING MULTISANDER VERSION OF SANDER AMBER8
> Total processors = 16
> Number of groups = 16
>
> Looping over processors:
> WorldRank is the global PE rank
> NodeID is the local PE rank in current group
>
> Group = 0
> WorldRank = 0
> NodeID = 0
>
> Group = 1
> WorldRank = 1
> NodeID = 0
>
> Group = 2
> WorldRank = 2
> NodeID = 0
>
> Group = 3
> WorldRank = 3
> NodeID = 0
>
> Group = 4
> WorldRank = 4
> NodeID = 0
>
> Group = 5
> WorldRank = 5
> NodeID = 0
>
> Group = 6
> WorldRank = 6
> NodeID = 0
>
> Group = 7
> WorldRank = 7
> NodeID = 0
>
> Group = 8
> WorldRank = 8
> NodeID = 0
>
> Group = 9
> WorldRank = 9
> NodeID = 0
>
> Group = 10
> WorldRank = 10
> NodeID = 0
>
> Group = 11
> WorldRank = 11
> NodeID = 0
>
> Group = 12
> WorldRank = 12
> NodeID = 0
>
> Group = 13
> WorldRank = 13
> NodeID = 0
>
> Group = 14
> WorldRank = 14
> NodeID = 0
>
> Group = 15
> WorldRank = 15
> NodeID = 0
>
>getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
>
>
>************
>error (*.e)
>************
>forrtl: severe (24): end-of-file during read, unit 9,
>file /home/asantana/asv.299/spcrem_REP.rst.006
>Image PC Routine Line Source
>sander.REM 400000000049E880 Unknown Unknown Unknown
>sander.REM 400000000049D990 Unknown Unknown Unknown
>sander.REM 4000000000455EE0 Unknown Unknown Unknown
>sander.REM 40000000003C5140 Unknown Unknown Unknown
>sander.REM 40000000003C60B0 Unknown Unknown Unknown
>sander.REM 40000000003F7220 Unknown Unknown Unknown
>sander.REM 400000000011CA70 Unknown Unknown Unknown
>sander.REM 400000000007DD60 Unknown Unknown Unknown
>sander.REM 4000000000078AC0 Unknown Unknown Unknown
>sander.REM 40000000000052D0 Unknown Unknown Unknown
>libc.so.6.1 2000000000666990 Unknown Unknown Unknown
>sander.REM 4000000000004CC0 Unknown Unknown Unknown
>MPI: MPI_COMM_WORLD rank 6 has terminated without calling MPI_Finalize()
>MPI: aborting job
>
>What could be the problem???
>Can I restart this simulation?
>
>Also when I try to truncate the trajectory the process stop with the following
>error:
>
>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 ARG ILE PRO CYS CYS PRO VAL ASN LEU
> LYS ARG LEU LEU VAL VAL VAL VAL VAL VAL
> VAL LEU VAL VAL 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 spcrem_REP.mdcrd.001 1 167675
>Checking coordinates: spcrem_REP.mdcrd.001
>FYI ptraj(): trajin stop value (167675) is greater than the number of sets
>read in
>FYI ptraj(): Setting stop to the maximum value (167673)
>
>PTRAJ: trjout spcrem_REP.mdcrd.001c
>
>ERROR in dispatchToken: Token string "trjout" not found in tokenlist
>
>
>ERROR in dispatchToken: Token string "spcrem_rep.mdcrd.001c" not found in
>tokenlist
>
>FYI: No output trajectory specified (trajout), none will be saved.
>
>PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 167673 frames.
> Summary of I/O and actions follows:
>
>INPUT COORDINATE FILES
> File (spcrem_REP.mdcrd.001) is an AMBER trajectory with 167673 sets
>
>OUTPUT COORDINATE FILE
> NULL entry
>
>ACTIONS
> Stack is NULL
>
>Processing AMBER trajectory file spcrem_REP.mdcrd.001
>
>Set 1 .................................................
>Set 50 .................................................
>Set 100 .................................................
>Set 150 .................................................
>Set 200 .................................................
>Set 250 .................................................
>Set 300 .................................................
>Set 350 .................................................
>Set 400 .................................................
>Set 450 .................................................
>Set 500 .................................................
>Set 550 .................................................
>Set 600 .................................................
>Set 650 .................................................
>Set 700 .................................................
>Set 750 .................................................
>Set 800 .................................................
>Set 850 .................................................
>Set 900 .................................................
>Set 950 .................................................
>Set 1000 .................................................
>Set 1050 .................................................
>Set 1100 .................................................
>Set 1150 .................................................
>Set 1200 .................................................
>Set 1250 .................................................
>Set 1300 .................................................
>Set 1350 .................................................
>Set 1400 .................................................
>Set 1450 .................................................
>Set 1500 .................................................
>Set 1550 .................................................
>Set 1600 .................................................
>Set 1650 .................................................
>Set 1700 .................................................
>Set 1750 .................................................
>Set 1800 .................................................
>Set 1850 .................................................
>Set 1900 .................................................
>Set 1950 .................................................
>Set 2000 .................................................
>Set 2050 .................................................
>Set 2100 .................................................
>Set 2150 .................................................
>Set 2200 .................................................
>Set 2250 .................................................
>Set 2300 .................................................
>Set 2350 ...................................
>ERROR in readAmberTrajectory(): Set #2386 is corrupted ( 4.066 2)...
>
>
>
>PTRAJ: Successfully read in 2385 sets and processed 2385 sets.
> Dumping accumulated results (if any)
>
>How I can repair the data???
>I going to loose all the work???
>
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