[gmx-users] RMSD Calculation

[Alper Kucukural]

Thank you very much,
It is working very well. I also looked at the document but I could not find. 
How can I select CA atoms in command prompt? Because I will run this program 
inside of the another program so I need to run g_confrms without select a 
group from second structure part.

----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, December 26, 2005 16:28
Subject: Re: [gmx-users] RMSD Calculation


> 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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