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┤âŒâŒâŠâŽ½âŽ½Â°â”¤â”Œâ”Œâ‰¤ ⎼âŠâ–’â â‹â”¼ 250 ⎽âŠâ”œâŽ½ ▒┼â ⎻⎼⎺âŒâŠâŽ½âŽ½âŠâ 250 ⎽âŠâ”œâŽ½.
D┤└⎻â‹â”¼Â± â–’âŒâŒâ”¤â””┤┌▒├âŠâ ⎼âŠâŽ½â”¤â”Œâ”œâŽ½ (â‹Â° ▒┼≤)
PTRAJ RMS: â┤└⎻â‹â”¼Â± RMSâ ┴⎽ ├â‹â””⊠â▒├▒
PTRAJ RMS: â┤└⎻â‹â”¼Â± RMSâ ┴⎽ ├â‹â””⊠â▒├▒
[â”â‰â–’⎼⎼âŠâ”œâ”œ.▒┼▒├▒⎽⊠┼⎺_⎽▒┌├_⎻⎼⎺â_⎻├⎼▒┘]$
[â”â‰â–’⎼⎼âŠâ”œâ”œ.▒┼▒├▒⎽⊠┼⎺_⎽▒┌├_⎻⎼⎺â_⎻├⎼▒┘]$
[â”â‰â–’⎼⎼âŠâ”œâ”œ.▒┼▒├▒⎽⊠┼⎺_⎽▒┌├_⎻⎼⎺â_⎻├⎼▒┘]$
[â”â‰â–’⎼⎼âŠâ”œâ”œ.▒┼▒├▒⎽⊠┼⎺_⎽▒┌├_⎻⎼⎺â_⎻├⎼▒┘]$
[â”â‰â–’⎼⎼âŠâ”œâ”œ.▒┼▒├▒⎽⊠┼⎺_⎽▒┌├_⎻⎼⎺â_⎻├⎼▒┘]$
---------------------------------
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Received on Fri May 26 2006 - 21:05:24 PDT
