From: Meric Ayse Ovacik (movacik_at_KU.EDU.TR)
Date: Sun Oct 17 2004 - 09:27:23 CDT
I am trying to simulate the small protein in vacuum without any boundary condition, containing PRO GLU and LEU respectively. Minimization took place properly with 500 steps. However, when I start MD there is the error: constraint failure in RATTLE algorithm for atom 36!
Then I disabled the rattle alg and tried to simulate again. The minimization was successful again, but this time I got the Bug alert: bad global exclusion count.
So I checked all the messages and read all the known bugs and troubleshooting pages.
The problem is the H atom bounded to N in LEU is too close to the bound between N and C in other words, the H atom is located somewhere where it should not be. Therefore I thought maybe there is something wrong with the parameter file... However another interesting thing is, when I start the minimization from another initial coordinates the simulation works fine!!!
So please help because I do not have any idea.
Ayse Meric Ovacik
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