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
