Hi,
The 'hbond' command from cpptraj has no particular trouble dealing
with nucleic acid systems. If you don't want intramolecular hydrogen
bonds you need to specify the 'nointramol' keyword. See the manual for
full details.
-Dan
On Mon, Jan 29, 2018 at 10:26 AM, Kenneth Huang
<kennethneltharion.gmail.com> wrote:
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 01 2018 - 06:30:03 PST
