[gmx-users] fitting

Erik Lindahl lindahl at stanford.edu
Thu May 23 21:41:06 CEST 2002

rams at poori.biochem.uiowa.edu wrote:

>Hello All,
>This is driving me crazy.
>I have a pdb file that I generate from a gro file of a protein.
>I have a 1ns trr file and the tpr file from there.
>I want to fit all the structures from the tpr file on to the pdb file I
>already have.
>It says in the manual that you can use g_rms or trjconv to fit to a
>reference structure.  How do i say what the reference structure is

No need to go crazy - just ask for help with "g_rms -h" :-)

(It's in the manpage section of the manual too) Then you'll get:


g_rms compares two structures by computing the root mean square deviation
(RMSD), the size-independent 'rho' similarity parameter (rho) or the 
scaled rho
(rhosc), reference Maiorov & Crippen, PROTEINS 22, 273 (1995). This is 
by -what.

Each structure from a trajectory (-f) is compared to a reference 
structure from
a run input file by least-squares fitting the structures on top of each 
-----> The reference structure is taken from the structure file (-s).

With option -mir also a comparison with the mirror image of the reference
structure is calculated.

Option -prev produces the comparison with a previous frame.

Option -m produces a matrix in .xpm format of comparison values of each
structure in the trajectory with respect to each other structure. This 
file can
be visualized with for instance xv and can be converted to postscript with

All the structures are fitted pairwise.

With -f2, the 'other structures' are taken from a second trajectory.

Option -bin does a binary dump of the comparison matrix.

Option -bm produces a matrix of average bond angle deviations analogously to
the -m option. Only bonds between atoms in the comparison group are 



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