[gmx-users] RMSD Calculation

[David van der Spoel]

Alper Kucukural wrote:
> Hi,
> I have just installed Gromacs-3.3 successfully. I want to calculate RMSD 
> value between two pdb files. I already wrote a program to select some 
> parts in pdb files. For example I select 1,6,7,15... CA Atoms in first 
> pdb file and 4,8,9,10... CA Atoms in second pdb file. Ofcourse the list 
> size is equal and I want to superimpose these proteins and find RMSD 
> value. Is it possible to send me an example how I can do this with 
> Gromacs-3.3.
g_confrms -f1 -f2 -n1 -n2

> Thanks in advance...
>  
> Alper Kucukural
> Phd in Biological Sciences and Bioengineering
> Sabanci University
> Istanbul/Turkiye
>  
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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