Re: [AMBER] RMSD vs reference substructure

From: Thomas Cheatham <>
Date: Tue, 9 Nov 2010 07:45:14 -0700 (Mountain Standard Time)

> trajin trajectory-without-solvent.x
> reference coarse-grained-structure.pdb
> rms reference rmsd-output-file.dat .P,C4',C2
> I can understand the warnings, but I thought it is possible to use an incomplete
> reference structure. Am I attempting to do something impossible? If not,
> what is the correct way of doing it?

The documentation may not be clear, however there still has to be a 1-1
mapping sequentially in the order of the atoms (i.e. you can use a
truncated reference, for example without water but not one that attempts
to hit every other atom). I admit this is not explained well, however
here is how you can overcome...

Either build a reference that has all the DNA atoms listed but only
accurate coordinates for P, C4', C2; or easier, build a new
trajectory-without-solvent.x that has only P, C4', C2, i.e. like you
stripped the water, strip every atom except for P, C4', and C2. To use
ptraj with this new stripped trajectory, load up a pdb file instead of a
prmtop when running ptraj. --tec3

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Received on Tue Nov 09 2010 - 07:00:13 PST
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