Thanks for the clarification.
For the vdw-removing step of solvation free energy calculation,
prmtop/inpcrd files of V0 and V1 are solute+watbox and watbox_only. In
addition, scmask of V0 should specify all the atoms of the solute. Is that
correct?
On Tue, Mar 15, 2011 at 3:31 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> the crucial concept here is that Amber will use two end state prmtop
> files, V0 and V1 to generate the actual intermediate, lambda-dependent,
> states on the fly during the simulation. Your input files will therefore
> be the same for all lambda-values (except clambda of course).
>
> > 1. Step 1: removing charge on H6 of BNZ. The input file difference
> between
> > V0 and V1 is the crgmask (except for clambda). What about intermediate
> > steps? Should I use the same crgmask as V1, so that AMBER would know what
> > atoms are associated with clambda transformation?
>
> each step in that transformation, no matter at what lambda will have the
> same crgmask in mdin.V0 and another one in mdin.V1
>
> > 2. Similarly, what are crgmask and scmask supposed to be for the
> > intermediate steps with clambda ranging from 0.1 to 0.9? And which prmtop
> > file should these substeps be using?
>
> crgmask and scmask define a whole transformation. they will not change
> from lambda-window to lambda-window. Likewise, only the end state prmtops
> must be supplied.
>
> > 3. For solvation free energy calculation, is one prmtop file enough for
> > both
> > charge-removing and vdw-removing if softcore potential is applied?
>
> no, a vdw-removing step always implies using two prmtop files.
> Effectively, even for a charge-removal step, you use two different
> topology/parameter sets but you need not build an extra prmtop and can use
> crgmask instead.
>
> 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 Tue Mar 15 2011 - 15:30:05 PDT
