Dear David,
Thank you very much for your advices:
> It looks like a weird bug in LEaP. If you really need to do this
particular
> calculation, you might have to upgrade to Amber 9 (which doesn't use
> perturbed prmtop files any more).
Still by using AMBER8, I compared two types of files, each of which is in
the
presence or absence of perturbation. As a result, in the file including
perturbation
the bond information was lost. So, I transferred the lost (bond) information
parts
toward the file including the perturbation. But I detected the following
error in the
initial phase of the sander calculation;
EXTRA_PTS: too many nghbrs
I searched AMBER Archive, and found the a related issue as follows;
http://archive.ambermd.org/200406/0261.html
According to it, I should modify a file of "extra_pts.f" for TIP5P. But I
cannot
see further detailed information for the modification in the Arichive. So,
if you
would you tell me how to rewrite the program in the case of the TIP5P water
model, I would much appreciate it.
Thank you very much in advance for your help.
best regards,
Sugino
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Received on Wed Jan 17 2007 - 06:08:40 PST
