AMBER Archive (2008)

Subject: Re: AMBER: Dihedral: ptraj

From: waqasuddin.khan_at_iccs.edu
Date: Thu Sep 18 2008 - 04:14:50 CDT

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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