RE: AMBER: perturbed atoms are not bonded on using TIP5P wate

From: sugino tatsuro <>
Date: Wed, 17 Jan 2007 14:47:51 +0900

Dear David,


Thank you very much for your advices:

> It looks like a weird bug in LEaP. If you really need to do this

> 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

presence or absence of perturbation. As a result, in the file including

the bond information was lost. So, I transferred the lost (bond) information

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;


According to it, I should modify a file of "extra_pts.f" for TIP5P. But I

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,


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Received on Wed Jan 17 2007 - 06:08:40 PST
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