[MMTK] Controlling orientation of two molecules

Kamilla Kopec ozero22 at yahoo.co.uk
Mon Oct 12 08:33:59 UTC 2009

Dear all, 

I am new to MMTK (3/4 hours experience so far!) and to python, so I need some pointers on building a very simple system. 

I am trying to build a  universe consisting of  an indole ring and a water molecule.  I have managed to do this by adding indole to the molecule database and using  universe.addObject(Molecule(indole)) and  universe.addObject(Molecule(water)) to create the required objects.  But this just places the water molecule at the preset coordinates in the database file. 

Instead, I would like to control the relative position of the two: placing the water molecule at a specific position relative the N-H group of the indole ring. In the script that I am writing I need to place the water molecule in the same plane as the N-H group as shown below and then move it away from the N-H moeity in 0.1 Ang increments by extending/shorting the H...O distance.  

H1   H2
  \    / 
Does anyone have any suggestions on how I could achieve this - I have checked out the manual and the EMBO tutorial, but I couldn't progress beyond getting two objects into the universe. I couldn't find anything about how to control/ manipulate the positions of one objects relative to another. 

Any help much appreciated.


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