Hi,
If you mean interactions bridged by a watermolecule, Protein-H2O-DNA,
then I don't know of any gromacs related tools for this. You need to
write your own tool for this. One way would be to multiply the existence
functions for hbonds between protein and water and the hbonds between
water and DNA, then use Justin's script to get the percentage.
Erik
leila karami skrev 2010-11-24 15.42:
Dear Justin
thanks for your attention
with chang of hbond.ndx file my problem was solved.
I have another question about g_hbond: if I want to obtain same
information (percentage of existence of each hbond during my
trajectory) about water mediated hydrogen bonds between protein and
dna, for obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool,
what groups should be select?
in previous state (protein-dna direct hydrogen bond), I selected 1)
protein and 2) dna.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
