On Tue, Jan 20, 2015 at 2:39 PM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> Thank you very much.
> Follow up question: what happened to inp? Whenever I use inp=2, I get
> wildly inconsistent results, for example ranging from -9 to +75 to +110 for
> a system that should have around -110. In fact, I cannot reproduce the
> results of the MMPBSA tutorial on the website if I use inp=2. inp=1, on the
> other hand, gives more "reasonable" results and can reproduce the tutorial.
> Is there a specific combination of parameters I should be using with inp=2?
> Because just taking the sample input file from the tutorial does not seem
> to work.
>
inp=1 is the more 'prototypical' SASA-based model. It's the same model
that GBSA uses, except the surface area algorithm is different. But results
are very similar.
inp=2 is a completely different model. It's still SASA-based, but has
separate attractive (dispersion) and repulsive (cavitation) terms. The
tutorial was written before the development of the inp=2 model (or at least
before inp=2 became the default), which is why inp=1 more closely agrees
with the tutorial.
If you are having problems with inp=2, you are certainly not the first, and
I would suggest switching to inp=1.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 20 2015 - 12:00:06 PST
