[AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed

From: MASAOKI FUJII <sj0018pv.ed.ritsumei.ac.jp>
Date: Thu, 16 Jul 2015 16:37:37 +0900 (JST)

Hi Amber community,

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.

Please tell me a method for solving a problem.

Masaoki Fujii
Master's program in advanced life sciences
Bioinfomatics course
Ritsumeikan University
1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan

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Received on Thu Jul 16 2015 - 01:00:02 PDT
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