AMBER Archive (2006)

Subject: Re: AMBER: trouble stripping waters with ptraj

From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Tue May 16 2006 - 15:17:32 CDT

Hi,

It seems like you are trying to read the stripped trajectory with
original topology file which contains waters. Try loading it with a
topology file just describing the protein without waters.

I hope this helps,

Asim Okur 

-- 
Asim Okur
Stony Brook University
Chemistry Department
Stony Brook, NY 11794-3400
631 - 632 1560

Adam Pelzer wrote:
> 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 
> <http://us.rd.yahoo.com/evt=40762/*http://www.yahoo.com/preview>. 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