On 9/17/10 5:37 PM, Justin A. Lemkul wrote:
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.
In theory you could get an approximate number from analyzing what polar
groups are not hydrogen bonded intramolecularly. There is not ready tool
to do this. The quickest solution is probably to rerun the simulation.
In most cases human time is more valuable than computer time.
-Justin
thank you in advance for your time
Fahimeh
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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