Dear Amber users,
I am trying to use the ptraj hbond facility to analyze lifetimes of
hydrogen bonds in a protein and between a protein and a ligand. More
precisely, I am trying to define a set of donors and have ptraj printing
out all Hbonds formed by these donors in at least 1 frame of the
trajectory (with the donor-acceptor distance, angle, occupancy etc -
see script below). However the output of this script is null. Maybe
somebody can give me a hint what am I doing wrong here.
I used to do this type of analysis with CARNAL and it always worked
pretty nice but since now I am using ptraj for almost all analysis, I
thought of using ptraj for this one as well. However, all the examples
that I found an the amber archive were about solvent interactions in
which the definition of donor and acceptors were exact.
Best wishes
vlad
trajin file.mdcrd
donor mask
:47,76,78-84,94,192,193,216,260,264,268,336,361,468.NZ,N,NE,NH1,NH2,ND2,OG1
acceptor mask :1-467.O* .H*
hbond distance 3.2 angle 60.0 series hbonds.dat
go
--
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru.eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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Received on Wed Oct 04 2006 - 06:07:17 PDT
