Thomas Cheatham wrote:
>>> donor mask :ADE.N1
>>> *acceptor mask :THY.N3 :THY.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
arrangement.
Regards
Reinhard Klement
--
Reinhard Klement
Max-Planck-Institut für biophysikalische Chemie
Abteilung Molekulare Biologie
Am Fassberg 11
D-37077 Göttingen
GERMANY
phone: +49 551 201 1389
fax: +49 551 201 1467
e-mail: Reinhard.Klement.mpibpc.mpg.de
Web: http://www.mpibpc.mpg.de/abteilungen/060
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Oct 12 2006 - 20:36:03 PDT
