summary for program for superimposing (small) molecules and new question

Dear netters:
I have received quite a lot of answers to my query about
Windows programs to superimpose molecules and calculate
the RMSD. Below is the summary of answers I've received.
Thanks a lot to everybody!!!! I have not tried yet all the
suggestions, but I found that QMol on the free side, and
Hyperchem and CaChe on the non-free side can do the
job quite easily.
Before I present the summary, I was to ask the (neccessary)
follow-up question:  In your experience, when a comparison
of an experimental molecular structure (i.e. X-rays) and its
calculated (Gaussian) counterpart is done, which will be the
treshold RMSD value which can be considered acceptable ?
Thanks in advance
                                  Dr. Daniel Glossman-Mitnik
From Jim Kress:
can do this.
From Ataualpa Albert Carmo Braga:
Hi Daniel,

Look for molden (

See you,

From Ray Merewheter:
if you only want to do it once or just a few times, you can sort the
output coordinate files in Excel by x, y, and z and then brute force
the alignment of any difficult atoms and do your own RMS.  pdb format
is particularly easy to understand.
From Jason D. Gans:

Qmol, available from the CCL software repository

can superimpose molecules and compute RMS deviation.


Jason Gans

B division
Los Alamos National Lab

From Brian Bennion:

VMD will do this fairly easily and is free

From Olalla Nieto Faza:
I don't know whether it can be used for small molecules as well, but
SwissPDB viewer (you can download it from  the server)
can make structure alignments of proteins and give you the RMS.
Hope it helps,
From Dr. Richard L. Wood:
Hi Dr. Glossman-Mitnik

I assume the two molecules are the same.  If so, couldn't you
open the files in MS Excel and calculate the RMSD that way?

Hope this helps.


From Nicolas Saettel:
I would be very interested too. So far the only workaround I found was to
reorder the Zmatrix in Molden and put all the xyz coordinates in 1 file... but
no RMS deviation!
Nicolas Saettel
From Elmar Gerwalin:
Hello Daniel,

"quatfit" does what you need.
It gives the RMS-deviation of 2 structures.
It's a simple C-Programm that should be installable on any platform with a
C-Compiler. (I'm using it on LINUX without problems)

You may find it using "google" or another search engine.

I append the src-code to my mail in case you can't find it.

Hope that helps.

From Giulio Vistoli:
Dear Daniel
Our VEGA program ( is able to superimpose two o more
molecules defining the opportune match atoms (with a graphical interface)
Best regards
Giulio Vistoli
From Juan Alexander Padron:
Dear Dr. Glossman-Mitnik:

I would extremelly apreciate if you could send me the replies to your
question about this topic, because I am interested in the same problem
(actually I am programming something like it and I need to know what
have been done). A propo, I think that DS viewer pro from Accelrys do
the trick (specially with the DS ViewerPro Molecular Overlay module) but
it is quite expensive (around 600 USD for the program, one copy, plus
the cost of the module).

Best Regards,

Juan Alexander Padrón García, PhD Student
Laboratorio de Química Computacional y Teórica
Facultad de Química
Universidad de la Habana
padrongj[at], alex2473[at]
From András Borosy:
Dear Dr Glossman-Mitnik,

Try the Windows version of MOE from CCG or MOLOC (!

Best wishes,

András Borosy

Dr. Daniel Glossman-Mitnik
Centro de Investigación en Materiales Avanzados (CIMAV)
LAQUICOM - Laboratorio de Química Computacional
Miguel de Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - MEXICO
Tel.: (52) 614 4391151
FAX: (52) 614 4391112
E-mail: daniel.glossman[at]