Hello.
Is this strange bug fixed?
http://archive.ambermd.org/201509/0399.html
I am still getting the same problem as described. Currently using CPPTRAJ ver. 15.
My input file (case1):
trajin ../combine_traj/combine-every-10ps-production.nc
center :1-400
image familiar
reference ../../min2_worst.rst
rms reference out backbonermsfit_all :1-400.C,CA,N,O
Output (showing only part of it):
2: [rms first out backbonermsfit_all :1-400.C,CA,N,O]
Target mask: [:1-400.C,CA,N,O](1600)
But if my input file (case2)=
trajin ../combine_traj/combine-every-10ps-production.nc
center :1-400
image familiar
reference ../../min2_worst.rst
rms first out backbonermsfit_all :1-400.C,CA,N,O
output (showing only part of it):
2: [rms first out backbonermsfit_all :1-400.C,CA,N,O]
Target mask: [:1-400.C,CA,N,O](1600)
Reference mask: [:1-400.C,CA,N,O](1600)
Does this means that in case 1, the rmsd calculation is not rmsfit to the reference structure? and in case 2, it is rmsfit into the first frame of the input trajectory instead of my reference structure - min2_worst.rst?
For the atomicfluct, if rms reference command put before atomicfluct, the calculation will rmsfit to the reference structure, right?
My input:
trajin ../combine_traj/combine-every-10ps-production.nc
center :1-400
image familiar
reference ../../min2_worst.rst
rms reference
atomicfluct out backbonermsfluct_all :1-400.C,CA,N,O byres
atomicfluct out backbonermsfluct_all.arg :1-400.C,CA,N,O byres
atomicfluct out backbonermsfluct_all.gnu :1-400.C,CA,N,O byres
atomicfluct out backbonermsfluct_rec :1-394.C,CA,N,O byres
atomicfluct out backbonermsfluct_rec.arg :1-394.C,CA,N,O byres
atomicfluct out backbonermsfluct_rec.gnu :1-394.C,CA,N,O byres
atomicfluct out backbonermsfluct_pep :395-400.C,CA,N,O byres
atomicfluct out backbonermsfluct_pep.arg :395-400.C,CA,N,O byres
atomicfluct out backbonermsfluct_pep.gnu :395-400.C,CA,N,O byres
atomicfluct out backbonermsfluct_activesite :395-400<:4.0 byres
go
Pls advise.
Thank you very much!!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 26 2016 - 02:30:03 PDT
