Hi,
why don't you use mm-pbsa? mm-gbsa is not *that* accurate and I am doubting
you will get meaningful dG.
per igb=8, which ambertools version you are using? Did this tests pass for
sander?
cd $AMBERHOME/test/gbneck2nu && make
Hai
On Tue, Jun 27, 2017 at 11:18 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> Hi all,
>
> We're trying to do some tests to compare mm-pbsa and mm-gbsa calculations
> for a protein/DNA complex. We've now got our mm-pbsa calculations mostly
> working. For the mm-gbsa calculation, in our &gb section of the mmgbsa.in
> script to MMPBSA.py we are trying igb=5 and igb=8 (both with mbondi2 for
> the radius set, though we've also tried mbondi3 for the igb=8 case). In the
> igb=5 case we are getting a negative dG, while using igb=8 with either
> mbondi2 or mbondi3 we are getting very positive dG values. I've seen some
> previous discussions here about folks having some difficulty with mm-gbsa
> for protein/nucleic complexes, but it seemed that those were prior to the
> optimized nucleic gb parameters of igb=8. Can anyone provide any input on
> whether mm-gbsa is a reasonable approach for relative dG's with either of
> these GB models? Thanks for your input.
>
> Kind regards,
> Joe
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Received on Tue Jun 27 2017 - 20:30:03 PDT
