Hello,
I am performing a simulation of a docked complex of
protein-ligand(cellotriose) using AMBER12. For the initial settings such as
minimization and equilibration I am following this tutorial :
http://www.ii.uib.no/~slars/bioinfocourse/PDFs/amber_tutorial.pdf. I
prepared the ligand using GLYCAM_06 forcefield and for protein I used
ff99SB. While running the equilibration step, I am getting the following
error:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 392 803 804
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
After looking into the list, I found that there might be some problem with
my system. But, I viewed the system in Pymol and everything looked fine to
me. I have attached all the .out file here:
https://drive.google.com/open?id=0B6ehLXK0eP7sYVZKd1FCUjk2VmM
Could anybody tell me what is going wrong with the system?
--
*Best Regards*
BM
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Received on Fri Jun 24 2016 - 04:00:02 PDT
