Re: AMBER: rmsd calculation in ptraj II

From: David A. Case <>
Date: Sat, 10 Mar 2007 21:55:32 -0800

On Sat, Mar 10, 2007, gurpreet singh wrote:
> i m using ptraj module of amber9 to calculate the rmsd( backbone only) over
> the whole trajectory of the simulation taking the crystal structure as the
> reference and i m getting values in the range of 35 to 38 although there is
> no significant change in the structure during the simulation. To verify
> the results i calculated the rmsd of the individual structure using VMD and
> their the rmsd is coming fine as expected.
> the command which i used in ptraj was:
> strip :WAT
> reference my crystal structure.pdb
> rms reference out rmsbackbone.dat :1-339.CA

Have you looked really carefully at the ptraj output? You still are not
giving the "real" ptraj input. The reference structure should be a pdb file
that is created by Amber (LEaP or ambpdb), not something directly from the
pdb. Ptraj will tell you how many atoms your mask matches, it looks like it
should be 339.

Try exploring different things: don't strip the waters, use the first frame
rather than a reference structure, use a restart file as input, rather than a
trajectory file, etc. The idea is to see if you can narrow down the problem.

...good luck....dac

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Received on Sun Mar 11 2007 - 06:07:42 PDT
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