AMBER Archive (2006)

Subject: Re: AMBER: RE: trouble stripping waters with ptraj

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri May 26 2006 - 06:28:35 CDT

maybe one of the characters that it wrote at the end was
some control character that changed your terminal properties.

Adam Pelzer wrote:

> 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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