On Thu, Aug 20, 2015, anu chandra wrote:
> Do we have any utility in latest versions of Amber, which do calculations
> what 'anal' did in older versions of Amber?. In other words, is it possible
> to do group decomposition of energy in MMPBSA.py, i.e total interaction
> energy between two groups, say group A (residue 1-100) and group B (residue
> 200-250) or group A (residue 50 ) and group B (residue 200-250)?. I noticed
> that 'anal' does this sort of decomposition of total energy and I wonder
> why Amber has completely removed 'anal' from its 10th version onwards.
Neither of the two common types of Amber force-fields (i.e. non-periodic
GB/PB/RISM, or periodic simluations with PME) are pairwise decomposable.
So the kind of analysis that the "anal" program carried out (which assumed
a pairwise energy function) are no longer very useful.
There are approximate ways to carry out energy decomposition using MM-GBSA
which might serve your purposes. Others on the list know a lot more about
these options than I do.
....dac
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Received on Thu Aug 20 2015 - 05:30:04 PDT
