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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Received on Wed Feb 24 2016 - 06:30:03 PST
