Re: [AMBER] correct way of imaging for rdf

From: Daniel Roe <>
Date: Thu, 23 Jan 2014 09:28:22 -0700


On Thu, Jan 23, 2014 at 9:06 AM, Jio M <> wrote:

> I have a linear long molecule around 120 angs and am using truncated
> octahedron water box.

What are your box dimensions?

> I am trying to test imaging on single restart file with cpptraj (for
> analysis of traj files for RMS mass weighted and radial distrubution of
> ions.)
> When I use:
> trajin
> autoimage
> trajout test.pdb pdb
> My linear molecule is out of box partially and looks "broken"! (but it is
> not broken if I just check the rst and prmtop in vmd)

Since PDB files don't have bond information VMD has to guess where the
bonds are, which can lead to things looking broken. Either use the prmtop
with the PDB in VMD or better yet write a mol2 file (which has bond info).

> I tried:
> trajin
> autoimage :253-269
> trajout test.pdb pdb
> 253-269 are residues in one molecule and it shows nice unbroken structure
> though whole structure does not look (visually in vmd) in

Without knowing more details about your system (is there one 'solute'
molecule or multiple?) it's tough to comment here. In general, for
autoimage to work properly you should pick as the 'anchor' molecule the
molecule that has the shortest distance to all other 'fixed' molecules;
autoimage by default assumes the first molecule should be used as the

> 1) What image processing should be done for RDF calculations and ofcourse
> I can use same traj for RMS analysis. I mean the molecule should be in
> center if RDF analysis to be done correcly.

No worries here - unless you specify 'noimage' to 'radial', imaging is done
for you.

> 2) Also as in ptraj I did not find 'mass' flag with cpptraj for rms
> calculations? can it be used in cpptraj as in ptraj

The 'mass' keyword has always been supported in the 'rms' command in
cpptraj (see the manual or internal help).

> 3) In section 8.9, Page number 230 AmberTools13 manual, the 'rmsd' and
> 'rms' are different things?

They are the same command; 'rms' is supported for backwards compatibility.


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) 585-6208 (Fax)
AMBER mailing list
Received on Thu Jan 23 2014 - 08:30:04 PST
Custom Search