[gmx-users] RMSD Calculation

[David van der Spoel]

Alper Kucukural wrote:
> 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.
You have to generate index files for the Ca that you want, you can do 
this with make_ndx. All the programs that read from the standard input 
can be controlled using redirects, e.g.:
echo "3 3" | g_confrms
> 
> ----- 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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> 
> 
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++