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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Received on Fri Jun 24 2016 - 01:00:02 PDT
