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
--
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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|