unbinding SMD skill question

From: Sangbae Lee (sblee_at_chem.ufl.edu)
Date: Wed Aug 19 2009 - 15:24:59 CDT

Hi, NAMDers.

All tutorial files that I could find out in NAMD website is for CV-SMD and
CF-SMD about "unfolding" or "stretching" or "expansion" of target molecule.

I could look at those tutorials at "stretching Deca-Alanine" case or
"namd-tutorial-files" for UBQ.

In my understanding, In basic SMD skill, we have to specify two groups of
atoms (fixed atom and smd atom). I think this is very useful for any
stretching or unfolding method.

But..

What I want to know is the tutorial or skill for the binding/unbinding of
any ligand (or substrate) from parent enzyme or protein.

I found so many journals about unbinding of substrate or ligand from protein
or enzyme, but I couldn't find how I can do practically.

When I try to unbinding my substrate from my enzyme, I don't understand what
skill I can apply.

Could you let me know it?

Thanks in advance.

Sblee

 

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