Fahimeh Baftizadeh Baghal wrote:
hello,
I have a trajectory generated by gromacs in which I excluded water and
there is only protein, now I like to see how does the number of h_bond
between water and protein change during the trajectory. In fact when I
use g_hbond I can choose the water and protein but I was wondering where
does the information about water come from??
Certainly you can choose whatever groups are present (either from default groups
or from those in an index file), but I would imagine the command will either
fail or simply identify that there are no hydrogen bond donors or acceptors
within what would otherwise be water.
If you have not saved the coordinates for water, you cannot run any command to
analyze properties related to or involving water.
-Justin
thank you in advance for your time
Fahimeh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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