[gmx-users] setting constraints to incomplete protein structures

[wk yeo]

Hello, all,

It is quite common to encounter protein structures in PDB which consist of only the catalytic domain (versus the structure of the entire protein). One such example is: http://www.pdb.org/pdb/explore.do?structureId=1H1W 

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?
2) Is there a way to constraint the atoms using Gromacs during MD at the points where the catalytic domain is 'chopped' from the rest of the protein?
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?

Thank you.

Regards,
wk yeo
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