Re: AMBER: align snapshots to a reference

From: Thomas E. Cheatham, III <>
Date: Wed, 30 Mar 2005 09:23:21 -0700 (Mountain Standard Time)

> 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

  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.


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Received on Wed Mar 30 2005 - 17:53:00 PST
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