Ms. Aswathy S wrote: > Dear Gromacs users, > > I am doing the MD of protein ligand complex. When I did the energy > minimization of this complex, in the result , the ligand molceule is moving > far away from the protein. > > What could be the possible reason? can anyone tell me how can i overcome this? >
Two possibilities come to my mind. 1. The parameters of the ligand are inappropriate, causing the ligand to be ejected from the active site. This is unlikely in a simple EM procedure, and probably would cause lots of LINCS or "blowing up" warnings. 2. More likely: Your protein is positioned near a box edge and the ligand is crossing periodic boundaries. Consider how you set up the box and read about PBC: http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions -Justin Here I dint get any error message as you mentoined in th first possiblity.Then about the seocnd suggestion, only two options provided to in the manual. pbd : no and pbc: xyz. I havn;t found any change in my problrm. can you rxplain a liitle bit more. waiting for you reply.... > Thanks in advance. > > Aswathy > Amrita School of biotechnology > Dept. Biotechnology > Ext. 3108 > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.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 gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin _______________________________________________ gmx-users mailing list [email protected] http://www.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
