Dear Amber users,
I've prepared my glycosylated metalloprotein using tleap and attempted minimization, heating and equilibration. Upon equilibration (having ntc = ntf = 2) I almost instantly get the following error:
vlimit exceeded for step 61; vmax = 27.0336
vlimit exceeded for step 62; vmax = 536.4434
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 5 6058 12494 12495
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
Atom 12494 is the O and atom 12495 the H1 of a Zn-coordinated water molecule (described using published forcefield parameters). Since the O and H1 are explicitly bonded I do not understand why SHAKE would want to constrain these bonds. Am I reading the error correctly? In parmed.py printBonds, printAngles, printDetails and printDihedrals for this water molecule all seem fine.
Could anyone please help me to solve this issue?
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Fri Sep 22 2017 - 06:00:05 PDT
