From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Feb 15 2012 - 15:27:12 CST
Dear Bruno,
1) Your site, www.boliveira.com, appears to be dead, so I couldn't see
the image.
2) Yes you can measure the VDW with NAMDEnergy, however you don't
mention electrostatics in your message. You may want to also
investigate the electrostatic interactions which predominate over VDW
at longer ranges.
Best,
Chris
On Thu, Feb 2, 2012 at 11:06 AM, Bruno Luís Pinto de Oliveira
<boliveira_at_itn.pt> wrote:
> 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
>
>
>
>
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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