Dear Amber users
I am interested to estimate the absolute binding free of a receptor R to a
ligand L using the soft core methodology.
The soft core will be used for the annihilation of L inside and outside of
receptor using an equivalent approach described in the amber tutorial
(second step, the vdw parameters change). However I have some concerns about
the topologies files used.
For instance for the association R:L, the topology file for the process V0
is obviously the topology file created with solvated R:L, but for V1 process
I am not sure that the topology file to be used is topology file created
only with R (without L). I am assuming that coordinates of two crd files for
both processes are identical apart of the coordinates of L.
This simulation will be carry on with atomic charges of L off and
consequently a positional restraint will be used. In this case I think
that its necessary to setup the dvdl_norest parameter (pag. 101 of amber
manual) to a value .ne. 0 in order the potential energy from positional
restraints will be not counted into DV/DL.
I would like to know the opinion of an expert in TI simulations
Thank you very much in advance for any help
Joao
--
*Joćo*
___________________________
*"Put your hand on a hot stove for a minute, and it seems like an hour. Sit
with a pretty girl for an*
* hour, and it seems like a minute. THAT'S relativity."*
(Albert Einstein)
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Received on Wed Oct 20 2010 - 04:30:04 PDT
