AMBER Archive (2008)

Subject: Re: AMBER: Dihedral: ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Sep 18 2008 - 04:04:24 CDT

maybe you could show us your inputs, it would help to see if there is a
mistake.

On Thu, Sep 18, 2008 at 2:39 AM, <waqasuddin.khan_at_iccs.edu> wrote:

> Hi,
>
> I want to determine the dihedral angle (bending behavior or twisting
> analysis) by running the ptraj file command. Whenever I run this command,
> it misses the first two trajectories (100ps each trajectory) while the
> rest of the trajectories runs smoothly.
>
> The error is:
>
> Error scanning a value: nno
> Residue labels:
>
> 63 .678 32 .397 45 .454 63 .249 31 .839
> 43 .741 64 .940 32 .044 44 .412 64 .648
> 33 .994 42 .456 64 .172 33 .187 41 .899
> 64 .440 34 .965 42 .006 66 .180 33 .757
> 42 .494 66 .732 34 .536 43 .020 66 .421
> 32 .792 42 .941 66 .621 33 .684 41 .500
> 62 .331 35 .939 44 .250 62 .322 36 .351
> 45
>
> Error scanning a value: ipres
> Error scanning a value: bonds with hydrogen, ICB
> Error scanning a value: bonds with hydrogen, IB
> Error scanning a value: bonds with hydrogen, JB
> Error scanning a value: angles with hydrogen, KT
> Error scanning a value: angles without hydrogen, KT
> Error scanning a value: dihedral w/ hydrogen, KP
> Error scanning a value: dihedral w/ hydrogen, JP
> Error scanning a value: dihedral w/ hydrogen, IP
> Error scanning a value: dihedral w/ hydrogen, ICP
> Error scanning a value: dihedral w/ hydrogen, LP
> Error scanning a value: dihedral w/out hydrogen, KP
> Error scanning a value: dihedral w/out hydrogen, JP
> Error scanning a value: dihedral w/out hydrogen, IP
> Error scanning a value: dihedral w/out hydrogen, ICP
> Error scanning a value: dihedral w/out hydrogen, LP
> Error scanning a value: join info
> Error scanning a value: irotat info
> Error scanning a value: box information, nspsol
> Error scanning a value: box information, nsp
> Scanning Cap; this has not been debugged!
> Scanning Perturbation info...
> Bonds...
> Error scanning a value: pert, ibper
> Error scanning a value: pert, ibper
> Error scanning a value: pert, ibper
> Error scanning a value: pert, ibper
> Error scanning a value: pert, icbper
> Angles...
> Error scanning a value: pert, ktper
> Error scanning a value: pert, itper
> Error scanning a value: pert, jtper
> Dihedrals...
> Error scanning a value: pert, kpper
> Error scanning a value: pert, icpper
>
> The same input file with the same residue labeling runs under ptraj
> command very nicely with its closely related homologue, but this can't
> work for this protein?????/!!!!!!!! What should I do now???
>
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