[gmx-users] Coordinates change after minimization
Ms. Aswathy S
aswathys at amritapuri.amrita.edu
Sat Jun 20 15:30:13 CEST 2009
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?
----- 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:
>> After minimizing the protein -ligand complex, the co-ordinates have
>> drastically.My idea about minimization was the coordinates will have
>> 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.
>> Thanks, Aswathy Dept. Biotechnology Ext. 3108
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