AMBER Archive (2008)

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

From: Qi Yan (kid1412_at_uab.edu)
Date: Tue Mar 25 2008 - 12:00:35 CDT

I think the .prmtop file I used is right. The issue may be the too big
size of trajectory. I just have one trajectory and some frame can not be
read by ptraj. Is there some method which can skip the error frame? If
not, does it mean I have to rerun it?

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Andrew Borgert
Sent: Tue 3/25/2008 10:11 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is
corrupted (-)
 
I ran into a similar problem recently. It turned out that I was using
an old .prmtop file that had the same solute but a different number of
waters in it. Have you tried visualizing you input trajectory with
something like VMD? If it looks very distorted after the first frame,
you are probably using the wrong .prmtop file.

Qi Yan wrote:
>
> 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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