Hi Thomas. I've done TI several times, and I always do what you mention:
saveamberparm system v0.prm v0.rst
delete system system.1
saveamberparm system v1.prm v1.rst
But this may be a problem when you are disappearing, say, one residue in a
stretch of RNA, since then you will end up with two separate pieces of RNA.
So, I am wondering, is it possible to do in the VDW step what one usually
does for the charge, i.e,
crgmask_v0=:10
scmask_v0=''
crgmask_v1=:10
scmask_v1=:10
while using the same prm and rst file for both V0 and V1? (in V0 you have a
residue 10 without charge but with VDW, while in V1 you have residue 10
without charge and without VDW).
Thanks,
Ignacio
On Fri, Mar 15, 2013 at 8:28 PM, <steinbrt.rci.rutgers.edu> wrote:
> 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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>
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Received on Mon Mar 18 2013 - 10:30:03 PDT
