[gmx-users] setting constraints to incomplete protein structures

wk yeo vivacity at hotmail.com
Mon Sep 29 22:33:02 CEST 2008

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.

wk yeo
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