AMBER Archive (2006)

Subject: AMBER: trouble stripping waters with ptraj

From: Adam Pelzer (yankeeswin314159_at_yahoo.com)
Date: Tue May 16 2006 - 15:09:30 CDT

Dear AMBER users,

I am new to using ptraj, and I just tried to strip the waters from a trajectory file ("sim_an_1000.mdcrd") to create a new trajectory file without waters ("sim_an_1000_water_stripped.mdcrd"). Initially it seemed to work, since ptraj processed all 200 frames of the trajectory file without complaints. However, when I tried to use sim_an_1000_water_stripped.mdcrd, I was told that the the file only contained 30 frames, and that the 31st was corrupted:

Processing AMBER trajectory file sim_an_1000_water_stripped .mdcrd

Set 1 ..............................
Set #31 appears corrupted (
 49.453 27.539 40.4013)

I am not sure whether the problem is with my input file or with the original trajectory file. I have cut and pasted my input file for stripping the waters below, as well as the output that is printed when I strip the waters. I would be very grateful for any suggestions on how to trouble-shoot this problem.

Thank you very much in advance for any advice.

Adam

Here's the input file:

trajin sim_an_1000.mdcrd
center
strip @5784-38092
trajout sim_an_1000_water_stripped.mdcrd trajectory nobox

  
Here's the output printed:

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 K+ K+ WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT WAT WAT WAT WAT WAT WAT
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...
Scanning Box
Read in box information...
Successfully completed readParm.

PTRAJ: Processing input file...
       Input is from standard input

PTRAJ: trajin sim_an_1000.mdcrd
Checking coordinates: sim_an_1000.mdcrd

PTRAJ: center
Mask [*] represents 38092 atoms

PTRAJ: strip @5784-38092
Mask [@5784-38092] represents 32309 atoms

PTRAJ: trajout sim_an_1000_water_stripped.mdcrd trajectory nobox

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 200 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (sim_an_1000.mdcrd) is an AMBER trajectory (with box info) with 200 sets

OUTPUT COORDINATE FILE
  File (sim_an_1000_water_stripped.mdcrd) is an AMBER trajectory

ACTIONS
  1> CENTER to box center via center of geometry, atom selection follows * (All atoms are selected)
  7> STRIP: 32309 atoms will be removed from trajectory: :377-11147

Processing AMBER trajectory file sim_an_1000.mdcrd

Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200

PTRAJ: Successfully read in 200 sets and processed 200 sets.
       Dumping accumulated results (if any)

                        
---------------------------------
Sneak preview the all-new Yahoo.com. It's not radically different. Just radically better.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu