[gmx-users] Re: Ligand is moving far away after energy minimization
Justin A. Lemkul
jalemkul at vt.edu
Thu Mar 5 13:07:56 CET 2009
Ms. Aswathy S wrote:
> 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:
> 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....
Given the information you've provided, no. If you can post the following
information, maybe things will be more clear on our end:
1. The *exact* commands given to set up your system
2. The contents of your .mdp file
>> Thanks in advance.
>> Amrita School of biotechnology
>> Dept. Biotechnology
>> Ext. 3108
>> gmx-users mailing list gmx-users at gromacs.org
>> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users