it's impossible to say from the output - we don't know how you generated
and equilibrated this structure.
a few comments, though:
- igb=5 performs poorly for RNA. Read Nguyen et al
https://www.ncbi.nlm.nih.gov/pubmed/26574454
- I would suggest using no cutoff (cut=9999), and not using nrespa=4
- your restraint inputs say "weak" but these are actually quite strong, and
you might want to make them weaker or reduce the time step.
- I think many of these are reflected in the high temperature of your
system - don't just wait for a failure, but if you see the system not
behaving as desired (temperature above 400, etc) then stop and look for
problems.
On Sat, Oct 1, 2016 at 7:40 AM, ABHIJEET CHOWDHURY <
f2013854.pilani.bits-pilani.ac.in> wrote:
> Dear AMBER users,
>
> I am trying to simulate a RNA duplex in an implicit solvent with igb=5
> but after some time into production, I get error saying
>
> " Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 233 677 678
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system."
>
> I am attaching the output file for more information. Can anyone
> suggest where to look for problem.
> PS: I had asked this question before but couldn't find that thread.
>
> Regards,
> Abhijeet Chowdhury
>
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>
>
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Received on Sat Oct 01 2016 - 06:00:02 PDT
