AMBER Archive (2008)

Subject: Re: AMBER: Dihedral: ptraj

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Sep 18 2008 - 04:32:38 CDT

no I mean everything, including the part where you tell it the prmtop. are
these exactly identical for the runs that work vs those that do not?
and it would help to see what ptraj says/does before the error part you
showed before.

On Thu, Sep 18, 2008 at 5:14 AM, <waqasuddin.khan_at_iccs.edu> wrote:

> trajin mm_md1_100ps_no_wat.mdcrd
> trajin mm_md2.mdcrd.gz
> trajin mm_md3.mdcrd.gz
> trajin mm_md4.mdcrd.gz
> trajin mm_md5.mdcrd.gz
> trajin mm_md6.mdcrd.gz
> trajin mm_md7.mdcrd.gz
> trajin mm_md8.mdcrd.gz
> trajin mm_md9.mdcrd.gz
> trajin mm_md10.mdcrd.gz
> dihedral dihedral_md :1-471 :132 :133-166 :167 mass out
> wd-2dihedral_mm_md.dat time 0.5
> strip :132-167
> strip :WAT
>
>
>
> here is the input file of my dihdral angle (ptraj)
>
> > 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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> >
>
>
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