Hi all,
I have a quick question about hbond analysis on protein-DNA systems. If I
do hbond on a a single residue to the entire DNA, ie
hbond ARG-DNA out hbond.ARG-DNA.dat :59,105-150 angle 135 dist 3.0 avgout
hbond_avg.ARG-DNA.out bridgeout hbond_brid.ARG-DNA.dat solventdonor :WAT
solventacceptor :WAT.O nointramol
#Frame ARG-DNA[UU] ARG-DNA[UV] ARG-DNA[Bridge]
1 47 319 7
2 43 325 15
3 46 329 14
4 49 322 16
The numbers seem inflated for a residue-DNA contact. If I do hbond analysis
on just the DNA alone though, and then subtract the relevant columns like
(HB of ARG+DNA) - (HB of DNA)
I get a much more reasonable looking set of numbers; am I correct in
assuming that hbond has trouble with dealing with DNA, or treats each DNA
strand as a different internal solute?
Best,
Kenneth
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Mon Jan 29 2018 - 07:30:03 PST
