AMBER Archive (2008)

Subject: RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)

From: Qi Yan (kid1412_at_uab.edu)
Date: Mon Mar 24 2008 - 15:50:40 CDT

Hi,All:

This is input file used:

trajin ***.mdcrd
strip :WAT
strip :Cl-
strip :Na+
image center
trajout ./****.mdcrd trajectory nobox

This is the output I get:
  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 9.0 integrated" (April 2006)
  -/- Executable is:
"/ibrixfs/apps/amber/intel/amber-9-64-openmpi/exe/ptraj"
  /-\
  \-/ Residue labels:

 GLU PRO VAL VAL TYR PHE LYS GLU GLN PHE
 .... GLU ASP ILE LEU ARG ASN LYS GLY CYS
 SER Cl- Na+ Cl- Na+ Cl- Na+ Cl- Na+ Cl-
 Na+ Cl- Na+ Cl- Na+ Cl- Na+ Cl- Na+ Cl-
 ...
 Na+ Cl- Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+
 Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+ Na+
 ...
 Na+ Na+ Na+ Na+ Na+ Na+ WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT WAT WAT

PTRAJ: Processing input from file test.in

PTRAJ: trajin production-Npt-300K_32CPU.mdcrd
  Checking coordinates: production-Npt-300K_32CPU.mdcrd

PTRAJ: strip :WAT
Mask [:WAT] represents 152781 atoms

PTRAJ: strip :Cl-
Mask [:Cl-] represents 76 atoms

PTRAJ: strip :Na+
Mask [:Na+] represents 109 atoms

PTRAJ: image center
Mask [*] represents 8466 atoms

PTRAJ: trajout ./complexfinal_2.mdcrd trajectory nobox

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 14991 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (production-Npt-300K_32CPU.mdcrd) is an AMBER trajectory (with
box info) with 14991 sets

OUTPUT COORDINATE FILE
  File (./complexfinal_2.mdcrd) is an AMBER trajectory

ACTIONS
  1> STRIP: 152781 atoms will be removed from trajectory: :727-51653
  7> STRIP: 76 atoms will be removed from trajectory:
:542,:544,:546,:548,:550,:552,:554,:556,:558,:560
    :562,:564,:566,:568,:570,:572,:574,:576,:578,:580
    :582,:584,:586,:588,:590,:592,:594,:596,:598,:600
    :602,:604,:606,:608,:610,:612,:614,:616,:618,:620
    :622,:624,:626,:628,:630,:632,:634,:636,:638,:640
    :642,:644,:646,:648,:650,:652,:654,:656,:658,:660
    :662,:664,:666,:668,:670,:672,:674,:676,:678,:680
    :682,:684,:686,:688,:690,:692
  7> STRIP: 109 atoms will be removed from trajectory: :542-650
  7> IMAGE by molecule to box center using the center of mass, atom
selection * (All atoms are selected)

Processing AMBER trajectory file production-Npt-300K_32CPU.mdcrd

Set 1 .................................................
... ...
Set 7918 .................
WARNING in readAmberTrajectory(): Set #7918 is corrupted ( 295.)...

PTRAJ: Successfully read in 7917 sets and processed 7917 sets.
       Dumping accumulated results (if any)

Does anybody know what is wrong with it?

Thanks in advance

Qi

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Da-Wei Li
Sent: Mon 3/24/2008 3:12 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is
corrupted (-)
 
Do you use ASCII format? If it is, you can simple read the file by
yourself.

I do not know exactly what happens but I fell there is sth wrong
associated with the file system(depend on the system you used). Pay
special care if your file size is large than 4G, in which case the 32
bit file pointer will meet overflow problem.

dawei

On Mon, Mar 24, 2008 at 3:01 PM, Qi Yan <kid1412_at_uab.edu> wrote:
>
>
>
> Hi,All:
>
> I got a trajectory file including 15000 frames and the file is 59G.
When I
> try to strip Water and Ions, I got the following WARNING message:
>
> WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)...
>
> PTRAJ: Successfully read in 7917 sets and processed 7917 sets.
> Dumping accumulated results (if any)
>
>
> Does it mean that only number 7918 frame is corrupted? Can I simply
ignore
> this frame? Actually, I don't know what is wrong with it. Does anybody
can
> help me out?
>
> Thanks in advance,
>
> Qi
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