Munazzah,
The issue starts with trying to read the trajectory file.
It seems that your file type is molfile (.mol) - can you provide details
about what you used to generate the trajectory, as AMBER does not write
that format (that I'm aware of).
Cheers,
Todd
On Thu, Dec 7, 2023 at 5:20 AM Munazzah Fatima Ansari via AMBER <
amber.ambermd.org> wrote:
> Hi Developers
>
> I am using plumed for trajectory analysis. I want to calculate radius of
> Gyration on C-alpha atom.
> For this I make a input file plumed.dat file as following:
>
>
> r: GYRATION ATOM=9, 28, 40, 61, 68, 79, 89, 113, 123, 133, 143, 153,
> 163, 180, 191, 215, 236, 243, 255, 274, 284, 295, 314, 331, 338, 348,
> 355, 365, 375, 390, 396, 403, 414, 421, 440, 446, 457, 467, 477, 487,
> 498, 509, 520, 544, 561, 575, 594, 614, 628, 638, 653, 668, 675, 692,
> 711, 732
>
>
> Then I run it with the following command:
>
>
> plumed driver --plumed plumed.dat --mf_crd md.mdcrd --natoms 30769
>
>
> But it gives me the error:
>
>
> DRIVER: Found molfile format trajectory crd with name md.mdcrd
> Problem reading CRD file
> PLUMED:
> PLUMED:
>
> ################################################################################
> PLUMED:
> PLUMED: (core/PlumedMain.cpp:618) virtual void
> PLMD::PlumedMain::cmd(const string&, const PLMD::TypesafePtr&)
> PLUMED: +++ assertion failed: initialized
> PLUMED: cmd("runFinalJobs") should be only used after plumed
> initialization
> PLUMED:
>
> ################################################################################
> PLUMED: Cycles
> Total Average Minimum Maximum
> PLUMED: 1
> 0.000130 0.000130 0.000130 0.000130
> terminate called after throwing an instance of
> 'PLMD::Plumed::ExceptionError'
> what():
> (core/PlumedMain.cpp:618) virtual void PLMD::PlumedMain::cmd(const
> string&, const PLMD::TypesafePtr&)
> +++ assertion failed: initialized
> cmd("runFinalJobs") should be only used after plumed initialization
> [pluto:900899] *** Process received signal ***
> [pluto:900899] Signal: Aborted (6)
> [pluto:900899] Signal code: (-6)
> [pluto:900899] [ 0] /lib64/libpthread.so.0(+0x12cf0)[0x7f2bca099cf0]
> [pluto:900899] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7f2bc9d10acf]
> [pluto:900899] [ 2] /lib64/libc.so.6(abort+0x127)[0x7f2bc9ce3ea5]
> [pluto:900899] [ 3] /lib64/libstdc++.so.6(+0x9009b)[0x7f2bca8d109b]
> [pluto:900899] [ 4] /lib64/libstdc++.so.6(+0x9654c)[0x7f2bca8d754c]
> [pluto:900899] [ 5] /lib64/libstdc++.so.6(+0x965a7)[0x7f2bca8d75a7]
> [pluto:900899] [ 6]
> /lib64/libstdc++.so.6(__cxa_rethrow+0x4d)[0x7f2bca8d785d]
> [pluto:900899] [ 7] plumed[0x4053e1]
> [pluto:900899] [ 8]
> /lib64/libc.so.6(__libc_start_main+0xe5)[0x7f2bc9cfcd85]
> [pluto:900899] [ 9] plumed[0x40560e]
> [pluto:900899] *** End of error message ***
> Aborted (core dumped)
>
>
> Please help me to understand why I'm getting this error.
>
>
>
> Munazzah
> Ph.D scholar
> RRCAT Indore,
> M.P. India
>
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>
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Received on Thu Dec 07 2023 - 07:30:03 PST
