VMD-L Mailing List

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Thu Oct 20 2011 - 06:15:37 CDT

Dear Pawel,

Thank you very much for your reply.

Maybe I'm not being clear enough and so I am not getting any help.

I published in my webpage the thermodynamic cycle of my transformation to be more easy to understand.

http://www.boliveira.com/NAMD.html

As I said in my transformation I did the set up such that the Re(CO)3 core vanished.

I was guessing that during the simulation the amines that are coordentated to the Rhenium will turn flexible and interact with the protein. What I see during the simulation is that the amines are still coordenated to the Rhenium and the rhenium core did not disappear.

Now I doubt if I did correctly the set up or if the set up is OK and the Re(CO)3 is presented during the simulation but in fact is not interacting with the protein ???

Lucky (or not) the caculated results are in good agreement with the experimental ones.

I found this information in the NAMD "manual":

"It is also worth noting that the free energy calculation does not alter intramolecular potentials, e.g.bond stretch,
valence angle deformation and torsions, in the course of the simulation..."

http://www.ks.uiuc.edu/Research/namd/2.6/ug/node36.html

That´s why I didn´t see the arms that are coordenated to the metal turning flexible?

Can anyone help me with some comments ??

Thank you very much for your help

Bruno