I've just got such an error when I forgot that I need to rebuild prmtop file if I strip water in the trajectory file.
So when you strip water or ions you should remember that the corresponding prmtop file should be made.
PS I am sorry to post into an old thread, but there wasn't such an answer in that thread.
Best regards,
Andrew
> 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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Received on Mon Aug 24 2009 - 11:11:10 PDT
