VMD-L Mailing List

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Thu Sep 08 2011 - 13:24:32 CDT

Dear all,

I'm did an alchemical FEP transformation of an inhibitor into another to calculate the free energy difference. The calculated values are in good agreement with the experimental values.

I have little experience with FEP calculations. I know that there is a plugin (ParseFEP) for the analisis of FEP. However I would like to visualize the transformation during the FEP simulation. I searched in the VMD mailing list for a procedure but I didn´t find any post about this subject or any information in the manual.

Is it possible???

How can I visualize the transformation of one inhibitor into another???

I have made myself clear?

Tks in advance

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