AMBER Archive (2004)

Subject: AMBER: SHAKE probelm

From: Huang, Hai (
Date: Fri Nov 19 2004 - 10:25:24 CST

Hi, all,

I am a new user of AMBER. I generated a crosslink of oligonucleotide and peptide with amber7. I try to simulate its structrure with molecular dynamics, it works well with SHAKE off (ntc=1, ntf=1), however, when SHAKE is turned on (ntc=2, ntf=2), the running crashs rapidly and error message appears:
     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 11 7 12 13

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

I have carefully checked the structure. LEAP doesn't report any error or warning. Does anyone have any idea about this problem? Thank you.

Hai Huang

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