[AMBER] hbond analysis on DNA-protein complex

From: Kenneth Huang <kennethneltharion.gmail.com>
Date: Mon, 29 Jan 2018 10:26:47 -0500

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

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?



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Received on Mon Jan 29 2018 - 07:30:03 PST
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