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

From: "Dr. Daniel Glossman-Mitnik" <daniel.glossman[at]cimav.edu.mx>
Date: Thu, 7 Aug 2003 12:30:34 -0500

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:

gOpenMol
  http://www.csc.fi/~laaksone/gopenmol/gopenmol.html

and

Tinker  
http://dasher.wustl.edu/tinker/

can do this.

***********************************************************************
> From Ataualpa Albert Carmo Braga:

Hi Daniel,

Look for molden (http://www.caos.kun.nl/~schaft/molden/windowsnt95.html)

See you,

Ataualpa.

***********************************************************************
> 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:

Hello,

Qmol, available from the CCL software repository

http://www.ccl.net/cca/software/MS-WIN95-NT/qmol/index.shtml

can superimpose molecules and compute RMS deviation.

Regards,

Jason Gans

B division
Los Alamos National Lab

********************************************************************************

> From Brian Bennion:

Hi

VMD will do this fairly easily and is free
www.ks.uiuc.edu/Research/VMD

Brian

*********************************************************************************
> 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 Expasy.org server) 
can make structure alignments of proteins and give you the RMS.
Hope it helps,
Regards

**************************************************************************************

> 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. 

Richard 

***************************************************************************************
> From Nicolas Saettel:

Hi,
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!
Cordially
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.
Bye
Elmar

**************************************************************************************************

> From Giulio Vistoli:

Dear Daniel

Our VEGA program (http://www.ddl.unimi.it) 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
e-mail: padrongj[at]fq.uh.cu, alex2473[at]yahoo.es
http://www.fq.uh.cu/investigacion/lqct/index.htm

*************************************************************************************************

> From András Borosy:

Dear Dr Glossman-Mitnik,

Try the Windows version of MOE from CCG or MOLOC (www.moloc.ch)!

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]cimav.edu.mx
            glossman[at]hotmail.com
            dglossman[at]yahoo.com
**********************************************************************

---

From: "Dr. Richard L. Wood" <rlw28-.at.-cornell.edu>
Date: Thu, 07 Aug 2003 14:57:35 -0500

I have a question as to how the program QMol calculates the RMSD of two
structures.

I used Excel to calculate the RMSD for two different conformations of
the same molecule and compared the result that I get using QMol, and I
get two different values, and I am wondering why that is.

In Excel, I calculated the distances between the same two atoms in the
two conformations, squared them, added them up, then divided by the
number of atoms.
After this, take the square root to get the RMSD.

It looks to me like QMol does something different.

Thanks in advance,
Richard

> From Jason D. Gans: Hello,
>

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist

---

From: Lubos Vrbka <shnek=at=chemi.muni.cz>
Date: Thu, 07 Aug 2003 22:52:03 +0200

> It looks to me like QMol does something different.

isn't it possible that QMol produces for example mass-weighted RMS or 
something similar? i can remember having similar problems (i.e. 
different values of the RMSD on the same set of structures) with some 
other programs (e.g. amber/ptraj, amber/carnal and vmd). maybe qmol 
could be some kind of similar case...

regards,
lubos

-- 
#################################################
Mgr. Lubos Vrbka
National Centre for Biomolecular Research
Masaryk university, Brno, Czech Republic

shnek=at=chemi.muni.cz
http://www.chemi.muni.cz/~shnek
tel. +420 541 129 508
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