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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
and
Tinker
can do this.
*********************************************************************** From Ataualpa Albert Carmo Braga:
***********************************************************************
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:
*********************************************************************************
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 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 ********************************************************************** |