Dear Charles,
I have been trying to use the HBDB in presence of explicit waters
(xplor scripting).
However there are some problems with the assignment/NBonded update
-
although I am using different segment names for protein and water
together with nmin, nmax and nseg (the last just seen in hbdb.inp test
example) together with segm (just seen under HBDB help),
I do not believe xplor does a proper selection of the segment.
firstly, there seems to be a limit on the number of residues / atoms: -
atoms beyond 4729 are not found {and on an energy update
the HBDB table is not filled}
-- I don't know what is special about that number, but since the complaint
is about a water which is not in the segment selected, I do not believe
the selection works.
if I reduce the number of waters in the simulation to get below this
number, xplor spends a good 2hrs+ on a reasonably fast pc on the energy
update
that is meant to give a hbond table - clearly this is not correct.
if I do the HBDB command/assignment before loading in the waters, it does
much better, now actually identifying the Hbonds and calculating the energy,
but it no longer sees Hbonds in energy updates after waters are added (i.e.
the psf
has been modified).
in conclusion I wonder whether there is a bug in the selection HBDB passes
on when there are multiple segments. {has this been tested?}
with best regards,
Matthias
Matthias Buck
Assistant Professor
Physiology & Biophysics Department
Case Western Reserve Univ.
Medical School, E646
2109 Adelbert Road
Cleveland, Ohio, 44106
fax 216-368-1693
phone 216-368-8651
e-mail [email protected]
http://mbalster.cwru.edu/
