AMBER Archive (2008)

Subject: AMBER: Dihedral: ptraj

From: waqasuddin.khan_at_iccs.edu
Date: Thu Sep 18 2008 - 01:39:33 CDT

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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