[gmx-users] Re: Ligand is moving far away after energy minimization
Ms. Aswathy S
aswathys at amritapuri.amrita.edu
Thu Mar 5 10:40:23 CET 2009
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....
> Thanks in advance.
> Amrita School of biotechnology
> Dept. Biotechnology
> Ext. 3108
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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