[gmx-users] Coordinates change after minimization

[Ms. Aswathy S]

using the g_confrm command the RMSD of the protein is 0 (Root mean square deviation after lsq fit = 4.14581e-08). It means the structure doesn't have a major change ultimately.. Please correct me if I am wrong..Can I move ahead with this minimization?

Dept. Biotechnology
Ext. 3108

----- Original Message -----
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [gmx-users] Coordinates change after minimization

Justin A. Lemkul wrote:
> 
> 
> Ms. Aswathy S wrote:
>> Hi,
>>
>> After minimizing the protein -ligand complex, the co-ordinates have 
>> changed
>> drastically.My idea about minimization was the coordinates will have 
>> minute
>> changes only. In this case my protein is completely transferring to a new
>> co-ordinates.Is that reasonable.??
> 
> The amount of change will depend on the quality of the initial model.  
> If large changes need to be made, they can be.  If the entire protein is 
> moving, then perhaps the box has not been prepared correctly, and the 
> translation is caused by a periodic jump.  Have a look at the output 
> (not just the coordinates) and see if you can deduce what's going on.
> 
Try running g_confrms to see whether they really are very different.

> -Justin
> 
>>
>> Thanks, Aswathy Dept. Biotechnology Ext. 3108 
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> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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