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 - 21:00:03 PDT
