Hi,
Probably as a starting point you'll want to look at solute-solvent
hydrogen bonding between your serine and water. Something like:
hbond Ser10 out nhbvtime.dat :10 avgout UU.dat \
solventdonor :WAT solventacceptor :WAT.O \
solvout UV.dat bridgeout Bridge.dat
should be enough to get you started. Consult the manual for more
details on the 'hbond' command.
-Dan
On Fri, Jun 24, 2016 at 1:58 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> Dear Amber experts,
>
> I know how to write cpptraj command for measuring over all productive MD
> simulation frames the distance between any two residues with fixed specified
> numbers as for instance between Ser10 and Wat 1000:
>
> distance res10_wat1000 :10.OG :1000.O out dist_res10_wat1000.agr
>
> I need now to analyze a possibility of bulk water molecules diffusion
> during MD simulation into and out the cavity inside protein
> and H-bond formation with Ser 10 residue located there.
> By the logic, I should identify in every MD frame the water molecule
> located at that instant time in a minimal inter-atomic distance
> between OG atom of Ser 10 and O atom of this water molecule.
> The measured distances must be saved in a file like dist_res10_wat_in_cavity.agr.
>
> I don't know how to modify the cpptraj command above to be relevant for the described
> water diffusion analysis.
>
> I would appreciate your help in correct formulation of the cpptraj command.
>
> Thank you,
> Michael
>
>
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jun 24 2016 - 11:00:02 PDT
