On Tue, 2014-03-04 at 00:29 +0800, Nitin Sharma wrote:
> Dear bill,
>
> Like you I used idecomp=2 but now I am confused regarding the output
> of "FINAL_DECOMP_MMPBSA.dat". I have attached the snapshots for the
> following queries:
>
>
> 1) As you can see in decomposition_1 which is my output using
> idecomp=2 is quite different from decomposition_tutorial which is
> result of idecomp=1 used in amber tutorial
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm . I would like to know what does this section "Total" in decomposition_1
"Total" is the sum of all energy components (Internal + van der Waals +
Electrostatic + Polar Solvation + Non-Polar Solv.). The 3 columns are
the average, std. dev., and std. err. of mean (just like the other
sections).
> signifies? Unlike other sections like van der waals, electrostatic it
> has only one sub-section Std. Err. of mean.
The "std. err. of mean" you are seeing actually belongs to the Non-Polar
Solv. The 3 "total" columns are unlabelled currently. I will look into
that and fix it.
> Also the difference between outputs I.e. decomposition_1 and
> decomposition_tutorial is due to different options selected or due to
> different versions of AMBER. I am using amber12
The comma-separated format was introduced after the tutorial was
written. You can set "csv_format=0" in the &decomp section to get the
same format as you see in the tutorial.
> 2) Secondly, what does delta section signifies? As can be seen
> from decomposition_2 only ligand i.e UNK 155 has significant value
It is the difference between the bound and unbound states (complex -
receptor - ligand). The "location" section tells you 'where' MMPBSA.py
thinks each residue is in the unbound state (R meaning the residue is in
the receptor and L meaning the residue is in the ligand).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Mar 03 2014 - 09:30:06 PST
