AMBER Archive (2006)

Subject: AMBER: RE: trouble stripping waters with ptraj

From: Adam Pelzer (yankeeswin314159_at_yahoo.com)
Date: Thu May 25 2006 - 23:50:53 CDT

 Thank you for your help on this. Originally things worked fine with using the files that I had created (the ones that had water and ions stripped), and I ignored the messages saying that the nonexistent frame following the final frame was corrupted. But recently I tried to run a job on a file with atoms stripped, and it gave the same error message, but the program also appeared to crash in some way. It was unable to give me the final few lines of output and instead gave me a mess of symbols, and I had to close the terminal to continue, since every time I hit enter I just got another mess of symbols. However, it produced the output files that it was supposed to (files showing the rmsd), and the output looks totally fine. Can I trust the output, even though the program crashed at the end?
 
 I've cut and pasted the input file and the printed output below. Thank you very much for your continued help on this; I really appreciate it.
 
 Adam
 
 Input file:
 reference no_salt_prod_avrg_no_wat.pdb
 trajin no_salt_prod_water_stripped.mdcrd
 center
 rms reference mass out no_salt_prod_avrg_pdb_all.rms time 2 @1-5783 name no_salt_prod_avrg_pdb_all_rms
 rms reference mass out no_salt_prod_avrg_pdb_2.rms time 2 :30-66 name no_salt_prod_avrg_pdb_2_rms
 
 
 Printed output:
 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...
  GLU THR THR ALA LEU VAL CYS ASP ASN GLY
  SER GLY LEU VAL LYS ALA GLY PHE ALA GLY
  ASP ASP ALA PRO ARG ALA VAL PHE PRO SER
  ILE VAL GLY ARG PRO ARG HIE GLN GLY VAL
  MET VAL GLY MET GLY GLN LYS ASP SER TYR
  VAL GLY ASP GLU ALA GLN SER LYS ARG GLY
  ILE LEU THR LEU LYS TYR PRO ILE GLU HIM
  GLY ILE ILE THR ASN TRP ASP ASP MET GLU
  LYS ILE TRP HID HIE THR PHE TYR ASN GLU
  LEU ARG VAL ALA PRO GLU GLU HIE PRO THR
  LEU LEU THR GLU ALA PRO LEU ASN PRO LYS
  ALA ASN ARG GLU LYS MET THR GLN ILE MET
  PHE GLU THR PHE ASN VAL PRO ALA MET TYR
  VAL ALA ILE GLN ALA VAL LEU SER LEU TYR
  ALA SER GLY ARG THR THR GLY ILE VAL LEU
  ASP SER GLY ASP GLY VAL THR HIE ASN VAL
  PRO ILE TYR GLU GLY TYR ALA LEU PRO HIE
  ALA ILE MET ARG LEU ASP LEU ALA GLY ARG
  ASP LEU THR ASP TYR LEU MET LYS ILE LEU
  THR GLU ARG GLY TYR SER PHE VAL THR THR
  ALA GLU ARG GLU ILE VAL ARG ASP ILE LYS
  GLU LYS LEU CYS TYR VAL ALA LEU ASP PHE
  GLU ASN GLU MET ALA THR ALA ALA SER SER
  SER SER LEU GLU LYS SER TYR GLU LEU PRO
  ASP GLY GLN VAL ILE THR ILE GLY ASN GLU
  ARG PHE ARG CYS PRO GLU THR LEU PHE GLN
  PRO SER PHE ILE GLY MET GLU SER ALA GLY
  ILE HIE GLU THR THR TYR ASN SER ILE MET
  LYS CYS ASP ILE ASP ILE ARG LYS ASP LEU
  TYR ALA ASN ASN VAL MET SER GLY GLY THR
  THR MET TYR PRO GLY ILE ALA ASP ARG MET
  GLN LYS GLU ILE THR ALA LEU ALA PRO SER
  THR MET LYS ILE LYS ILE ILE ALA PRO PRO
  GLU ARG LYS TYR SER VAL TRP ILE GLY GLY
  SER ILE LEU ALA SER LEU SER THR PHE GLN
  GLN MET TRP ILE THR LYS GLN GLU TYR ASP
  GLU ALA GLY PRO SER ILE VAL HIE ARG CA
  CA CA CA CA CA adp
 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: reference no_salt_prod_avrg_no_wat.pdb
 
 Processing PDB file no_salt_prod_avrg_no_wat.pdb
 
 PTRAJ: trajin no_salt_prod_water_stripped.mdcrd
 Checking coordinates: no_salt_prod_water_stripped.mdcrd
 
 PTRAJ: center
 Mask [*] represents 5783 atoms
 
 PTRAJ: rms reference mass out no_salt_prod_avrg_pdb_all.rms time 2 @1-5783 name no_salt_prod_avrg_pdb_all_rms
 Mask [@1-5783] represents 5783 atoms
 
 PTRAJ: rms reference mass out no_salt_prod_avrg_pdb_2.rms time 2 :30-66 name no_salt_prod_avrg_pdb_2_rms
 Mask [:30-66] represents 574 atoms
 FYI: No output trajectory specified (trajout), none will be saved.
 
 PTRAJ: Successfully read the input file.
        Coordinate processing will occur on 250 frames.
        Summary of I/O and actions follows:
 
 INPUT COORDINATE FILES
   File (no_salt_prod_water_stripped.mdcrd) is an AMBER trajectory with 250 sets
 
 OUTPUT COORDINATE FILE
   NULL entry
 
 REFERENCE FILE
   File (no_salt_prod_avrg_no_wat.pdb) is a PDB file
 
 ACTIONS
   1> CENTER to box center via center of geometry, atom selection follows * (All atoms are selected)
   7> RMS to reference structure (no_salt_prod_avrg_no_wat.pdb) using mass weighting
       Dumping RMSd vs. time (with time interval 2.00) to a file named no_salt_prod_avrg_pdb_all.rms
       Saving RMSd vs. time date to scalarStack entry no_salt_prod_avrg_pdb_all_rms
       Atom selection follows * (All atoms are selected)
   7> RMS to reference structure (no_salt_prod_avrg_no_wat.pdb) using mass weighting
       Dumping RMSd vs. time (with time interval 2.00) to a file named no_salt_prod_avrg_pdb_2.rms
       Saving RMSd vs. time date to scalarStack entry no_salt_prod_avrg_pdb_2_rms Atom selection follows :30-66
 
 
 Processing AMBER trajectory file no_salt_prod_water_stripped.mdcrd
 
 Set 1 .................................................
 Set 50 .................................................
 Set 100 .................................................
 Set 150 .................................................
 Set 200 .................................................
 Set 250
 ERROR in readAmberTrajectory(): Set #251 is corrupted (
 �����?�y% ��l?qO÷¼ ¿7)...
 
 
 
 PTRAJ: S┤␌␌␊⎽⎽°┤┌┌≤ ⎼␊▒␍ ␋┼ 250 ⎽␊├⎽ ▒┼␍ ⎻⎼⎺␌␊⎽⎽␊␍ 250 ⎽␊├⎽.
        D┤└⎻␋┼± ▒␌␌┤└┤┌▒├␊␍ ⎼␊⎽┤┌├⎽ (␋° ▒┼≤)
 
 PTRAJ RMS: ␍┤└⎻␋┼± RMS␍ ┴⎽ ├␋└␊ ␍▒├▒
 PTRAJ RMS: ␍┤└⎻␋┼± RMS␍ ┴⎽ ├␋└␊ ␍▒├▒
 [┐␉▒⎼⎼␊├├@▒┼▒├▒⎽␊ ┼⎺_⎽▒┌├_⎻⎼⎺␍_⎻├⎼▒┘]$
 [┐␉▒⎼⎼␊├├@▒┼▒├▒⎽␊ ┼⎺_⎽▒┌├_⎻⎼⎺␍_⎻├⎼▒┘]$
 [┐␉▒⎼⎼␊├├@▒┼▒├▒⎽␊ ┼⎺_⎽▒┌├_⎻⎼⎺␍_⎻├⎼▒┘]$
 [┐␉▒⎼⎼␊├├@▒┼▒├▒⎽␊ ┼⎺_⎽▒┌├_⎻⎼⎺␍_⎻├⎼▒┘]$
 [┐␉▒⎼⎼␊├├@▒┼▒├▒⎽␊ ┼⎺_⎽▒┌├_⎻⎼⎺␍_⎻├⎼▒┘]$
 
                
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