[gmx-users] setting constraints to incomplete protein structures

[wk yeo]

Hello,

My responses are as follows:

>> My questions:
>> 1) Is it a good idea to use such catalytic domain structures for MD simulation? Or should I only use complete protein structures for MD?
> That depends entirely upon what you are interested in simulating.

I am interested in predicting the binding energy (via further processing using a docking software) of a ligand to a specific protein target based on the conformation of the binding pocket after MD.  How will missing residues in the other parts of the protein target affect the MD run for such purposes?

>> 2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to constraint any atoms at the 'edges' during the MD run?
>
> What kind of "edges?" Those that are adjacent to the missing segments? If
> that's what you mean, see distance *restraints* or position *restraints*.

Yes, I meant atoms that are adjacent to the missing segments. When should I use distance restraints and when should I use position restraints?

I have a new question: What if the protein-ligand complex structure obtained from PDB contains chloride ions? How should I handle any ions during the MD runs? Restraint them as well? Or should I just let them go through MD without any restraints?

regards,
wk yeo
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