AMBER Archive (2005)

Subject: AMBER: MM_PBSA parameters

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Tue Dec 06 2005 - 09:26:55 CST


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Nelson Fonseca <nfonseca_at_dq.ua.pt>

Dear Amber users:

Our group is interested on the study of the binding interactions between ligands and receptors. These studies are carried by molecular dynamics in a wide range of organics solvents such as DMSO, methanol, CCl4 and ethanol. For the estimative of the binding energy associated with the bindng recognition process we are interested to use pos-processing methods such as MM-PBSA analysis. However on the best of our knowledge parameters for the non-polar contribution (Gnp) for these solvents (dmso,methanol, ethanol and CCl4) are not available from the literature. We would like to know if it is possible to apply the mm-pbsa methodoly to the simulations performed with these solvents. In other words there are parameters available for these solvents in order to use the mm-pbsa.in sripts type provided with amber 8.

Thanks in advance,

Nelson Fonseca Department of Chemistry University of Aveiro PORTUGAL


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