[gmx-users] g_rms -bm

[Kowsar Bagherzadeh]

Dear Justin
 
Thank you very muchh
 
Sogol


________________________________
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Kowsar Bagherzadeh <kw_bagherzadeh at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, May 24, 2012 9:59 AM
Subject: Re: [gmx-users] g_rms -bm



On 5/24/12 7:24 AM, Kowsar Bagherzadeh wrote:
> 
> 
> Dear Users,
> I am trying to analyze a ligand-protein simulation results. I read in the manual
> that using g_rms command with –bm option produces a matrix of average bond angle
> deviations. And only bonds between atoms in the comparison groups are
> considered. Does it mean that it is for the bonds and their angles that are
> already in existence? (Not the ones that may be formed throughout simulation, I
> mean the ligand may for example interact with residues through H-bonds) .I have

In this context, a "bond" means an actual chemical bond.  A hydrogen bond is a nonbonded interaction.

> made a group in my index file named Active site (including only the active site
> residues), and I have a LIG group as well. If I choose these two groups for
> g_rms with this command:
> /g_rms –s *.tpr –f *.trr –o rmsd.xvg –bm bond.xpm –n *.ndx**/
> Does it show me how the ligand affects the active site residues bond angles?

Potentially.

> And one more question, how can I study the ligand orientation in the active site?

That depends on how you define orientation - internal metrics like dihedrals or angles between planes of groups in the ligand, relative measurements like its position with respect to protein residues, etc.  All analysis tools are listed in the manual, Chapter 8 and Appendix D.  It's quite a lot to read, but you'll be able to identify all the various things you can analyze and how the information might be connected across different analysis routines.

-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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