[gmx-users] Re: distance restraint

pauladelgado pa-delga at uniandes.edu.co
Fri Sep 28 21:34:36 CEST 2012

This is the distance of one pair of atoms that i restraint. 
I apologize if i did't mention why i am using distance restraint, i am
working with a protein obtained using homology modelling, the next step
after i get the protein structure is doing molecular docking, the problem is
that i need to refine the structure and i found in literature that the
protein goes through a conformational change where it forms a bundle of 4
alfa helix (hydrofobic interactions) before it interacts with its ligand, so
besides of making the refinment of the structure i need  to obtain that
bundle in order to do molecular docking. The reason for doing the refinement
in vacuo is that when you minimize a struture to avoid steric clashes i
always make them in vacuo with other software, the problem is that i need to
form the bundle and the software i usually used doesn't handle position
restraint.  My intention never was to bother you,   I am very thankful for
your time to answer my questions.
Sorry for all the inconvenience


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