[gmx-users] RMSD average structure

[David van der Spoel]

On Mon, 2003-09-15 at 09:48, Andrea Carotti wrote:
>  
> Hi,
>     I have a long md run of 1800 frames and I' ve seen that it's ok.
> Now I'm trying to analyze it with g_rmsf to obtain an average
> structure with the b-factors (-ox option),
> and here i have problems.
> I obtain a protein structure with a lot of errors :bonds and rings of
> LEU, GLU, GLN, PHE, PRO, ARG, TYR are abnormal.

Isn't this just due to the averageing? It is quite common to get
unphysical structures... You can minimize the structure, or you can try
to find a structure in your trajectory that has least RMSD to your
average (a representative structure you could call that)

>  
> I've used this command line:
>  
> g_rmsf -f traj.xtc -s file.tpr -n index.ndx -ox average.pdb
>  
> The average.pdb appears like this:
> 
> HEADER Protein in water
> 
> REMARK THIS IS A SIMULATION BOX
> 
> CRYST1 82.099 82.107 82.106 70.53 109.47 70.53 P 1 1
> 
> MODEL 1
> 
> ATOM 1 N THR A 1 102.438 58.760 45.270 1.00425.29
> 
> ATOM 2 H1 THR A 1 102.405 58.965 45.305 1.00483.72
> 
> ATOM 3 H2 THR A 1 102.369 59.009 45.257 1.00481.60
> 
> ATOM 4 H3 THR A 1 102.347 59.001 45.283 1.00477.17
> 
> ATOM 5 CA THR A 1 102.708 57.777 45.222 1.00325.73
> 
> ATOM 6 CB THR A 1 102.648 57.636 44.219 1.00332.12
> 
> Anyone can help me? There is something I can do?
> 
> Thanks in advance
> 
> 
>  
> #############
> Andrea Carotti
> Dip. Farmaco-chimico
> Università di Bari
> via E. Orabona, 4
> CAP 70124
> e-mail : and.carotti at farmchim.uniba.it
> web: http://www.farmchim.uniba.it/samba/
> phone: +39080/5442638
> fax: +39080/5442230
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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