On Thu, Jul 16, 2015, MASAOKI FUJII wrote:
>
> I would like to do Molecular dynamics for O-GlcNAcylation proteins.
> first, i bonded between O-Linked β-N-acetylglucosamine (O-GlcNAc) and serin using "bond" command.
> second, i minimization for O-GlcNAcylation proteins without water.
> third, i ran simulation. but The following error showed.
>
> \\\\\\\\\\\\\\\\
> vlimit exceeded for step 0; vmax = 143.5315
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 6 3162 6372 6373
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> \\\\\\\\\\\\\\\\
There is not much information here. Look to see which atoms have numbers
6372 and 6373: that is where the problem is. Maybe that will help you
identify the problem.
Use the "checkValidity" command in parmed to look for problems in your setup.
Try a system with O-GlycNAc bonded to a short peptide, rather than a large
protein.
...good luck...dac
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Received on Thu Jul 16 2015 - 06:00:04 PDT
