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:
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....
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
-Justin
Thanks in advance.
Aswathy
Amrita School of biotechnology
Dept. Biotechnology
Ext. 3108
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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