Re: [AMBER] rmsd and hbond

From: Daniel Roe <>
Date: Mon, 9 Sep 2013 10:54:21 -0600


On Mon, Sep 9, 2013 at 3:20 AM, Mary Varughese <> wrote:
> Is there any need to do a "mass weighted backbone RMS fit of every frame to
> the first frame in the trajectory" before performing hbond analysis(by


> ptraj). Also on analysing solvent interaction with the system ( dsDNA). is
> it sufficient to reimage like (used iwrap=1)
> center :1-20 mass origin// dna
> image origin center familiar
> center :1-38 mass origin //Na ions
> image origin center familiar
> center :1-5529 mass origin// water residue
> image origin center familiar

This is incorrect, particularly the last 4 commands. First, I *highly*
recommend you use the 'autoimage' command in cpptraj for this; it was
specifically designed to take all of the guesswork out of re-imaging a
trajectory. However, if you're dead-set on doing it yourself, this has
worked for me in the past:

center :L-M origin mass
image center origin
center :L-N origin mass
image center origin

This assumes you have double-stranded DNA from residues L to N where L
is the first residue of your first DNA strand, M is the last residue
of the first strand, and N is the last residue of the second strand.

> Also if i have to strip water residues at a distance greater than 3.6
> angstrom;
> would it be ok to have all these in a single script.

It is if you do the stripping of the solvent last. Without knowing why
you want to strip the water though it's tough to make an exact
recommendation. See the 'mask' command in cpptraj for writing out
structures with distance-based masks. Also of interest may be the
'closest' command, which will keep a certain # of waters close to a
specified mask.

> I dont want to create another prmtop.

Unless you use the closest command or you are very lucky, if you strip
just based on distance there is no guarantee the resulting systems
will have the same # of atoms, so you will probably have to make
another topology to process these structures. The 'mask' command will
output PDB files which are essentially their own topology, so you may
have luck using that command.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Sep 09 2013 - 10:00:03 PDT
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