Re: [gmx-users] RMSD

Fri, 25 Jan 2013 00:44:17 -0800 


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....@gmail.com>
To: Discussion list for GROMACS users <gmx-users@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 <flormart...@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_arasteh2...@yahoo.com>
Para: Discussion list for GROMACS users <gmx-users@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 <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@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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