Please copy/paste your min.in and md.in files for minimization and heating.
Bill
On 9/22/17 7:08 AM, Daniel Roe wrote:
> 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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Received on Fri Sep 22 2017 - 07:30:03 PDT
