Hi,
On Thu, Mar 14, 2013 at 1:22 PM, Ahmed Ayoub <atayoub.ualberta.ca> wrote:
> calculation worked. The question is, is what I did by changing the type
> right or wrong? And is there another way to just let MMPBSA accept O3 as a
> type?
I don't think there is a definitive answer to this, but in my opinion
I think it might be OK since the O3 and O2 types are both phosphate
group oxygen. MMPBSA folks may want to correct me here, but I think
the only reason MMPBSA needs the atom type in this case is in
calculating the non-polar solvation term, and my suspicion is that the
O2 parameters are "good enough" for the O3 type in this calculation.
Caveat: if MMPBSA is using the atom type information for something
else however, it might not be OK.
-Dan
>
> Thanks a lot..
>
> Ahmed Ayoub
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University of Utah
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Received on Fri Mar 15 2013 - 08:30:02 PDT
