Thanks Jason . . .
On Wed, Oct 22, 2014 at 6:11 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Wed, 2014-10-22 at 16:05 +0530, Sourav Purohit wrote:
> > Hi All,
> >
> > In the Amber tutorial on Antechamber, while loading tleap, is it
> important
> > to load ff99SB? Will loading only GAFF not suffice??
>
> I presume you are talking about Tutorial B4 (Sustiva)? In that case,
> ff99SB is loaded because at some point it parametrizes the
> reverse-transcriptase enzyme with a bound sustiva. ff99SB is needed for
> the protein part of the complex (i.e., everything _except_ the sustiva
> residue).
>
> If you just want to create a prmtop file for the sustiva molecule by
> itself (no solvent, no protein, etc.), then only loading GAFF will
> suffice.
>
> However, leaprc.ff99SB loads solvent boxes and the protein force field.
> It's rare that you ever want _only_ the GAFF force field loaded...
>
> Of course there's another way to figure this out. Just try it... ;)
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Wed Oct 22 2014 - 06:00:05 PDT
