[gmx-users] RMSD

[Erik Marklund]

On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote:

>
>
> Thanks for your reply.
> I want to chose one of the 5 conformers from a NMR PDB. As I studied  
> in literature, the average structure could be selected regarding  
> RMSD values and the go on with selected one to simulate in in water,  
> lipid bilayer.
> All right, I may make a matrix, but how would I chose my purposed  
> conformers?
>
>
>  Thanks for all your suggestions.
>
> Sincerely,
> Shima
>
>
> ________________________________
> From: Leandro Bortot <leandro.obt at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, January 24, 2013 8:54 PM
> Subject: Re: [gmx-users] RMSD
>
>      you can make a simple script which calculates all the pairwise  
> RMSD
> values with g_rms. By doing this you can make a "RMSD matrix".

I think you can get the RMSD matrix from g_cluster in one go.

>
>      The usefulness of this depends on what you are trying to see,  
> which
> wasn't clearly stated to us. I did it once because I wanted to know  
> how
> similar the 20 conformers from a NMR PDB actually were.
>
>
>
> 2013/1/24 FLOR MARTINI <flormartini at yahoo.com.ar>
>
>> The values are OK, you obtain a value of RMSD of 0.2510229 . The  
>> value -1
>> refers time, and it is because you do not have a trajectory. You are
>> comparing only two .pdb structures, so it is consistent that you  
>> obtain
>> only one value, as you do not have more than one frame to compare.
>> Regards
>> Flor
>>
>> Dra.M.Florencia Martini
>> Cátedra de Farmacotecnia II
>> Facultad de Farmacia y Bioquímica
>> Universidad de Buenos Aires
>> Junín 956 6º (1113)
>> TE: 54 011 4964-8273
>>
>>
>> ________________________________
>>   De: Shima Arasteh <shima_arasteh2001 at yahoo.com>
>> Para: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Enviado: miércoles, 23 de enero de 2013 16:14
>> Asunto: Re: [gmx-users] RMSD
>>
>> What I see in xvg file is as below:
>>
>> # g_rms -s 1.pdb -f 2.pdb -o rmsd1.xvg
>> #
>> # g_rms is part of G R O M A C S:
>> #
>> # Gromacs Runs On Most of All Computer Systems
>> #
>> @    title "RMSD"
>> @    xaxis  label "Time (ps)"
>> @    yaxis  label "RMSD (nm)"
>> @TYPE xy
>> @ subtitle "Protein after lsq fit to Protein"
>>    -1.0000000    0.2510229
>>
>>
>> I though that -1 is the ref value and the other is the relative  
>> RMSD for
>> 2.pdb. Is this -1 should be positive? What is this -1? Would you  
>> give me
>> any suggestions   please?
>>
>>
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Cc:
>> Sent: Wednesday, January 23, 2013 9:36 PM
>> Subject: Re: [gmx-users] RMSD
>>
>>
>>
>> On 1/23/13 12:48 PM, Shima Arasteh wrote:
>>> I want to find the structure with the lowest RMSD, so I think it  
>>> does
>> not make different to set any of pdb files as the ref structure.
>>> I made an attempt and got the RMSD regarding the first pdb file. The
>> RMSD relative to -1 for the ref structure, is written in xvg file.  
>> Is my
>> approach logically correct?
>>>
>>
>> The RMSD value should be positive, so I don't know how you get -1.   
>> Your
>> approach does not seem very sound - a structure does not have an  
>> absolute
>> RMSD value; it has an RMSD value relative to a reference structure,  
>> which
>> must be some sort of meaningful comparison or else you're not really
>> measuring anything useful.
>>
>> -Justin
>>
>> -- ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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