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" <[email protected]> To: "Discussion list for GROMACS users" <[email protected]> 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 >> _______________________________________________ gmx-users mailing list >> [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the >> archive at http://www.gromacs.org/search before posting! Please don't >> post (un)subscribe requests to the list. Use the www interface >> or send it to [email protected]. Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> > -- 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 [email protected] [email protected] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
