On Mon, 2014-04-14 at 00:34 +0530, Sourav Purohit wrote:
> Hi All,
> One more question just to make sure that my procedure is correct.
> Th efollowing has been done in the MMPBSA tutorial:
>
> com = loadpdb ras-raf.pdb
> ras = loadpdb ras.pdb
> raf = loadpdb raf.pdb
>
> set default PBRadii mbondi2
>
> saveamberparm com ras-raf.prmtop ras-raf.inpcrd
> saveamberparm ras ras.prmtop ras.inpcrd
> saveamberparm raf raf.prmtop raf.inpcrd
>
> I wanted to know if the sequence of commands is fixed. i.e . will it be
> correct if I use the "set default PBRadii" command before loading the pdb
> files??
That's fine. The "set default PBRadii" command must be used before
"saveAmberParm", but other than that it doesn't matter when you use it.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 14 2014 - 05:00:03 PDT
