AMBER Archive (2005)

Subject: Re: AMBER: align snapshots to a reference

From: Wen Li (liw_at_wadsworth.org)
Date: Wed Mar 30 2005 - 13:52:34 CST

Dear Drs. Simmerling and Cheatham,

Thanks you both for your help.

I run the following input for ptraj:

trajin eq6.traj 10 135 100
reference ref.rst (restart file from amber)
trajout aligned_pdb pdb
rms ref.rst out rms @P
strip :Cl-
strip :Na+
go

Then, I got two aligned file, aligned10.pdb and aligned110.pdb. It seems
like that these two structures are aligned together, but both are far
away from the reference coordinates - I used ambpdb -p mytop < ref.rst >
ref.pdb

Here are the coordinates of the first line from the following files:

ref.pdb
ATOM 1 H5T RG5 1 38.720 16.214 81.045

aligned10.pdb
ATOM 1 H5T RG5 1 -4.310 27.117 -20.806 0.00 0.00

aligned110.pdb
ATOM 1 H5T RG5 1 -4.448 27.235 -16.973 0.00 0.00

When I used carnal to select the two snapshots (10th and 110th) from the
trajectory eq6.traj, and saved as pdb files. The following is their
coordinates of the first line:

traj.pdb.10
ATOM 1 H5T RG5 1 35.505 83.843 19.461

traj.pdb.110
ATOM 1 H5T RG5 1 35.534 85.483 26.438

Obviously, these coordinates are closer to the reference although they
were not as close each other as those obtained after the alignment.

I was hoping that you could help on this.

Thanks!

Wen

On Wed, 30 Mar 2005, Thomas E. Cheatham, III wrote:

>
> > I was hoping that you could make comments on if the following works for
> > the procedure that I described earlier:
> >
> > trajin MDtraj1 1 1000 100 (one snapshot from each 100)
> > reference my_reference_snap (a reference snapshot)
> > trajout aligned_traj (includes 1000/100 = 10 snapshots)
> > rms my_reference_snap out rms @P (for an RNA molecule)
> > strip :WAT
> > strip :Cl-
> > strip :Na+
> > go
>
> The easiest thing to do is to try it and see...
>
> Likely you want every 100th frame starting with the 100th, not the
> first:
>
> trajin MDtraj1 100 1000 100
>
> Do you want PDB files out or a new trajectory? If PDB,
>
> trajout aligned_pdb pdb
>
> Make sure that the reference PDB maps 1-1 with the input trajectory (at
> least for the atoms being matched, i.e. the reference in this case does
> not have to contain water, but should have the same number of RNA atoms in
> the same order); at present we do not have the capability implemented to
> have a separate prmtop/state for the reference coordinates.
>
> --tom
>
>
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