Hi,
> 1) Am I right if I assume that in hydration free energy calculations:
>
> V0 => refers the system containing solvent (common atoms) + solute (unique
> atoms), and
>
> V1 => refers the system containing solvent (common atoms) only?
>
> In that case, should it be correct to use for the V1 state just the
> coordinates and topology files containing ONLY the water solvent?:
yes, I always built that by doing
saveamberparm system v0.prm v0.rst
delete system system.1
saveamberparm system v1.prm v1.rst
if the system contains a solute (residue 1) and a water box.
> V0
>
> prmtop: solWat.top
>
> crgmask=':solute'
> scmask=':solute'
>
> ifsc=1
>
> V1
>
> prmtop: wat.top
>
> crgmask=''
> scmask=''
>
> ifsc=1
yes, that will be the way to run it.
> 2) And also, in the in gas phase transformation ("organic molecule" in
> vacuo into "nothing" in vacuo), what options should I specify in V0 and V1
> and what coordinate and topology files should I use for the end state?
You dont need to do this anymore. The tranformation keeps internal
energies intact, so the dG for solute->nothing always equals 0.0.
You do need to do the vacuum charge removal for the solute though. That
can be avoided by switching to one-step transformations if you want to.
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 Fri Mar 15 2013 - 18:00:02 PDT
