In addition to my previous message, I randomly chose a frame from a
trajectory, and add this frame to the beginning of the trajectory which I
want to align to the added first. The result is that the trajectory is not
aligned to the first frame:
trajin deleq6.traj 9 135 100
trajout align/aligned.pdb PDB
rms first out rms .P
go
On Fri, 1 Apr 2005, Wen Li wrote:
> Dear Dr. Cheatham,
>
> Thanks for your help. After change to use "rms reference out rms .P", the
> aligned frames still did not go to the reference - the coordinates are as
> the following:
>
> ambpdb -p nowater.top < trajB_eq10_2357.crd > align/2357.pdb
> 2357.pdb:
>
> ATOM 1 H5T RG5 1 38.720 16.214 81.045
> ATOM 2 O5* RG5 1 38.536 17.137 80.857
> ATOM 3 C5* RG5 1 37.509 17.739 81.667
>
> aligned9_pdb
>
> ATOM 1 H5T RG5 1 -7.741 6.288 30.532 0.00 0.00
> ATOM 2 O5' RG5 1 -8.666 6.420 30.309 0.00 0.00
> ATOM 3 C5' RG5 1 -9.451 6.562 31.393 0.00 0.00
>
> aligned_pdb.109
>
> ATOM 1 H5T RG5 1 -11.054 4.909 29.566 0.00 0.00
> ATOM 2 O5' RG5 1 -11.505 5.675 29.205 0.00 0.00
> ATOM 3 C5' RG5 1 -12.614 6.006 30.055 0.00 0.00
>
> Wen
>
>
> On Fri, 1 Apr 2005, Thomas E. Cheatham, III wrote:
>
> >
> > > trajin MDtraj1 1 1000 100
> > > reference my_reference_snap
> > > trajout aligned_traj
> > > rms my_reference_snap out rms .P
> >
> > The correct usage is
> >
> > rms reference out rms .P
> >
> > which will use the most recently specified reference file (prior to the
> > rms command).
> >
> >
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Received on Fri Apr 01 2005 - 21:53:00 PST
