Hi,
You may want to try cpptraj instead. Try the following input:
parm <your topology file>
trajin md.mdcrd
rog @9,28,40,61,… out rog.dat
run
Hope this helps,
-Dan
On Thu, Dec 7, 2023 at 6:18 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 - 06:30:03 PST
