[gmx-users] RMSD Calculation

[Alper Kucukural]

Dear Misha,
Thank you very much for your response,
Yes you are right, I am trying to find a solution to solve this problem but 
it is nice for me to learn such kind of tools on the other hand I will also 
check Swiss PDB viewer. If you know more please let me know.
Thanks in advance...
Alper Kucukural

----- Original Message ----- 
From: "Иванов Миша" <grasp2 at mail.ru>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Monday, December 26, 2005 19:50
Subject: Re[2]: [gmx-users] RMSD Calculation


Dear Alper,

Why have you chosen such a complicated way to superimpose two structures and 
to calculate RMSD. You may download free Swiss PDB viewer and to perform 
much more easier all the mentionned procedures there.

Misha Ivanov

-----Original Message-----
From: "Alper Kucukural" <alper at mindsventure.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Mon, 26 Dec 2005 17:00:09 +0100
Subject: Re: [gmx-users] RMSD Calculation

>
> 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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