Hi,
> As usually in double decoupling calculation, in V1 state, the ligand still
> remains, but just not interacted with protein( it is in gas state and
> usually contraint in origin position). So I still need the ligand in top
> and crd file. Dr. Donald Hamelberg suggested me to make a frcmod file and
> modify the vdw parameter to 0.0, but this will also did not calculate the
> ligand intramolecular interaction. I am wondering is there other way for
> just turn off the vdw interaction?
> Thanks !
what Prof. Case said is nevertheless correct. Amber's softcore TI
implementation requires a setup e.g. like this:
pmrtop V0: Protein+Ligand+Solvent
prmtop V1: Protein+Solvent
so the end state system prmtop does not contain the ligand. Since you run
the calculation using groupsander on both prmtops, your ligand will still
be 'there' at lambda=1, but it will not interact with anything else (but
maintains its internal potentials).
The alternative way of using 'dummy' atoms (with zero vdW parameters) will
also work in principle, but is discouraged due to potential severe
simulation instabilities (all described in more detail in the two Amber
softcore papers).
So what you want to do is certainly possible in Amber. Check out the
recommended tutorial. It can be adapted for absolute binding free
energies, but setting the restraints (in the V1 side of the system)
requires some planning, since they will be linearly scaled. The manual has
more on this, see the dvdl_norest option.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Jan 02 2012 - 04:00:02 PST
