If your only use of gb is for post-processing, you can just generate a new
prmtop with the radii you want and use that for post-processing. You would
only consider rerunning if the radii were used during md. If you did
standard md in explicit solvent the radii were not used so do not matter
for the md part.
On Apr 16, 2016 10:30 PM, "Jag Silwal" <jagsilwal.gmail.com> wrote:
> Dear all,
>
> I used "PBRadii mbondi 2" while generating topology and coordinate files in
> X-leap. I need to run MMPB/GBSA analysis after simulations. Based on the
> amber manual igb =8 is the best for proteins but now I can't use igb=8 for
> GBSA because manual says that we have to use igb=2 or 5 for PBRadii
> mbondi=2 setup.
>
> I already ran MMPB/GBSA analysis with igb=5 but I was wondering if:
>
> a) There is a way to simply change the PBRadii mbondi to 3 without having
> to rerun the whole simulation again?
>
> b) I already ran PB/GB and alanine mutagenesis calculation using igb=5. I
> am guessing I need to rerun the calculation once the PBRadii is changed.
> right?
>
> Any helpful suggestions would be appreciated,
>
> Jag,
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Received on Sat Apr 16 2016 - 21:00:04 PDT
