Hi,
Your version of cpptraj is wildly out of date. Please upgrade to AmberTools 15.
-Dan
On Wed, Feb 24, 2016 at 7:01 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> I have done 30 ns md simulation using amber11. I am having issue, while plotting RMS fluctuations. The cpptraj script that I used for generating RMS fluctuation is as follows:
>> rmsf.in
> trajin itk1.mdcrd.gz
> trajin itk2.mdcrd.gz
> trajin itk3.mdcrd.gz
> trajin itk4.mdcrd.gz
> trajin itk5.mdcrd.gz
> center :1-263
> image familiar
> strip :WAT
> strip :NA+
> rms first out itk-apo.rmsd .C,CA,N time 2.0
> atomicfluct out itk-apormsf.apf .C,CA,N byres
>> cpptraj command run
> cpptraj -p itk.prmtop -i rmsf.in
> I have encountered following error.
>
>>CPPTRAJ: Trajectory Analysis. V1.0.5
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from file rmsf_test.in
> [trajin ../itk1.mdcrd]
> [trajin ../itk2.mdcrd]
> [trajin ../itk3.mdcrd]
> [trajin ../itk4.mdcrd]
> [trajin ../itk5.mdcrd]
> Error: Could not predict # frames in ../itk5.mdcrd. This usually indicates
> a corrupted trajectory. Frames will be read until EOF.
> [trajin ../itk6.mdcrd]
> [trajin ../itk7.mdcrd]
> [trajin ../itk8.mdcrd]
> [trajin ../itk9.mdcrd]
> [trajin ../itk10.mdcrd]
> [center :1-263]
> [image familiar]
> [strip :WAT]
> [strip :NA+]
> [atomicfluct out itk.fluct.dat :1-263.CA byatom]
> Warning: Unknown Command atomicfluct.
>
> Why is this this strange behavior observed? Any suggestions would be very helpful. Thank you.
> Best Regards, Saman Yousuf AliJunior Research Fellow,
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 24 2016 - 07:30:06 PST
