AMBER Archive (2005)

Subject: Re: AMBER: trajectory alignment using ptraj

From: Wen Li (liw_at_wadsworth.org)
Date: Fri Apr 01 2005 - 12:42:36 CST

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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