Subject: RMS on atoms position calculation

From: Pierre Mignon <[email-masked]>
Date: Tue, 18 Dec 2001 17:30:34 +0100

Hello everyone, i'd like to thank some CCLers for their answers upon a program for RMS on atoms position calculation. Here are the answers.
Pierre Mignon

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Try MOLMOL:
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

Best regards,

Andrus

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On Tue, 18 Dec 2001, Pierre Mignon wrote:

>>Hello everyone,
>>I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ?
>>Thank's in advance.
>
g_confrms is part of gromacs www.gromacs.org
but you cannot get it separate.

I'm sure someone has a server out there somewhere...

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
[email-masked]	[email-masked]   http://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Hi,

>> I'd like to do calculation of the RMS difference of two conformations for one system. Does someone know how to get such a program freely ?
>

in the CCL archives is such a program, called "quatfit" (the fitting is done using quaternions).
It is a command line driven C program, you have to compile yourself.
Input files have to be in xmol format.
The documentation covers all this. BTW, quatfit has been programmed by J.Labanowsky, the CCL administrator.

Regards,

Anselm

--
_______________________________________________________________________
Anselm Horn, Dipl. Chem. Univ.          [email-masked]
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_______________________________________________________________________

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Try Quatfit available at CCL.net

Best regards,
Tomek

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Dear Pierre,

If I remember well Andrew Martin's ProFit can calculate the rmsd between
two structures (both small molecules and proteins). It is free for
academics and you should be able to download it from:
  http://www.bioinf.org.uk/
(got to Software and then ProFit).

It was written for proteins but I have used it in the past for ligands
only.

Good luck,

Irilenia

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Dear Pierre,

try Tinkers superpose !

Thomas Strassner

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Hi, 

So, you can use GopenMol or Moilview to do it. I think GopenMol is the
better one...
Pascal
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Dear Pierre,

why don't you try our "Server for Pairwise Superposition of Protein 3D
Structures and Analysis of Conformational Changes" at :

http://www.ucmb.ulb.ac.be/~ocha/wwwsup1/wwwsup.cgi

Bye,

L.
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Does someone know how to get such a program freely ?

MOLMOL
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
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