On Fri, Sep 22, 2017 at 8:30 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> 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.
When you specify ntc = 2, *all* bonds to hydrogen are constrained. The
vlimit errors indicate your system is blowing up. It may be worthwhile
to re-run the MD and print out energies and trajectory frames every
step so you can see what is happening in more detail (especially
because it happens so quickly the file sizes should remain
reasonable). What may be happening is that the H of the water ends up
having a bad overlap with the Zn and shoots off into oblivion or
something. One thing you could try to go is check for bad overlaps in
your initial structure using the 'check' command from cpptraj:
https://github.com/Amber-MD/cpptraj. You may need more minimization
before running your MD phase.
-Dan
>
> 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Sep 22 2017 - 07:30:02 PDT
