AMBER Archive (2006)

Subject: Re: AMBER: ptraj hbond analysis troubles

From: Reinhard Klement (
Date: Wed Oct 11 2006 - 03:25:27 CDT

Thomas Cheatham wrote:
>>> donor mask :ADE_at_N1
>>> *acceptor mask :THY_at_N3 :THY_at_H3*
>>> hbond distance 7 series hbond
>>> trajout traj.peptide nobox
> p.s. that duplex is fairly big for simulation and contains a lot of
> mismatches, G-G, C-C, A-A, T-T; I hope that is what you want... The G-G
> and A-A overlaps may be severe enough to lead to stability problems in MD
> unless minimized appropriately.
Besides all the trouble assigning proper masks for H bond analysis in
ptraj (and some confusion about donors and acceptors ;-) ) I am not
quite sure what kind of DNA structure you want to simulate. You created
a double stranded B-form DNA which contains mostly homo base pairs (i.e.
GG, CC, AA, TT ). Many of these non canonical base pairs occur in
"parallel-stranded"(ps) DNA. psDNA in general does not adopt a B
conformation. Proper base pairing of homo base pairs (and others) is
described in a publication by Hobza & Sandorfy, JACS, 1987, 109,
1302-1307 but these base pairing schemes need some special backbone

Reinhard Klement

Reinhard Klement
Max-Planck-Institut für biophysikalische Chemie
Abteilung Molekulare Biologie
Am Fassberg 11
D-37077 Göttingen


phone: +49 551 201 1389 fax: +49 551 201 1467



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