NAMDenergy plugin_van der Waal interactions

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Thu Feb 02 2012 - 11:06:20 CST

Hi everyone,

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 Rhenium(CO)3 core. The rest of the molecules is the same. Please find an image here for clarification:

http://www.boliveira.com/NAMD4.html

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 active site (worst inhibitor).

I would like to know if I can use the NAMDenergy plugin to analyse the vdwaal 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 vdwaal energy = more stable = less repulsion and more positive vdwaal = less stable = more repulsion).

If not can someone suggest me another aproach to trying to get an understanding of the contributions to protein-ligand stabilities.

Thank you

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:10 CST