VMD-L Mailing List

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Wed Feb 08 2012 - 10:05:41 CST

Hi everyone,

I realized that my webpage was down. Perhaps this was the reason no one answered me. Or perhaps the question didn't make a lot of sense.

I will try again ;)

I am simulating two organometallic coumpounds, which are very similar, complexed with the same protein (iNOS).

The differences between the compounds is on the type of atoms that are coordenating the Metal(CO)3 core. The rest of the molecules is the same. Please find an image here for clarification:

https://docs.google.com/document/pub?id=1HJfQqiTfEAko6sxo4PlXf9KkKeOIVKPdQrCtlpxTdrs

In one case the Rhenium(CO)3 is well accomodated inside the active pocket (better inhibitor), while in the ohter case after 3ns the Rhenium(CO)3 is oriented toward the peripheral pocket situated at the surface of the enzyme (worst inhibitor).

I would like to know if I can use the NAMDenergy plugin to analyse the vdwaals interactions between the Rhenium(CO)3 part and the residues of the active pocket to indentify which residues contribute for the repulsion or stability of the Re(CO)3? (considering that less positive vdwaals energy = more stable = less repulsion; more positive vdwaals = less stable = more repulsion).

If not can someone suggest me please another approach to trying to get an understanding why in one case the Re(CO)3 core is accomodated inside the active pocket and in the other case is repulsed.

Thank you in advance

Regards

.....................................................................................................................................................
Bruno L. Oliveira
Radiopharmaceutical Sciences Group
Chemistry Department , ITN
http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
http://www.boliveira.com