Hello everyone,
I want to calculate the effect of incorporating
ions in the grooves and backbones of a double stranded DNA molecule in the
hydrogen bonding between the two chains constituting the DNA. I want to
calculate the number, distance distribution and the lifetime of H- bonding
between base pairs of two chains both in presence and in absence of the
sodium ion. As far as I know, from the g_hbond utility of GROMACS we can
calculate the hydrogen bond related parameters but I am not quite sure with
the indexing. My index group looks like-
Group 0 ( System) has 97135 elements
Group 1 ( DNA) has 758 elements
Group 2 ( NA) has 624 elements
Group 3 ( CL) has 602 elements
Group 4 ( Water) has 95151 elements
Group 5 ( SOL) has 95151 elements
Group 6 ( non-Water) has 1984 elements
Group 7 ( Ion) has 1226 elements
Group 8 ( NA) has 624 elements
Group 9 ( CL) has 602 elements
Group 10 ( Water_and_ions) has 96377 elements
Group 11 ( major) has 376 elements
Group 12 ( minor) has 256 elements
Group 13 ( chain_A) has 379 elements
Group 14 ( chain_B) has 379 elements
Group 15 ( chain_A_Na) has 1 elements
Group 16 (chain_A_chain_A_Na) has 380 elements
Group 17 ( backbone) has 258 elements
I decomposed the entire DNA molecule into two segments, chain_A and chain_B
so that I can calculate the H-bonding parameters between the two chains.
But I dont know what to do when I want to check the H-bonding between
chain_A and chain_B in presence of sodium. Should I make a separate group
of chainA and Na (say chain_A_Na) and then calculate the h-bonding with
chain_B? Am I doing anything wrong? Is it supposed to be done in some other
ways? Please help me out with this.Thanks in advance.
Regards,
Soumadwip Ghosh
Senior research fellow,
Indian Institute of Technology, Bombay
India.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
