On Mon, Jun 27, 2016, bharat gupta wrote:
First: if you reply to a digest mail (that contains lots of messages), please
delete all the non-relevant material. Otherwise, it is very hard to even
find your question.
> > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > deviation is too large
> > > NITER, NIT, LL, I and J are : 0 2 392 803 804
> >
> > The problem is at atoms 803 and 804. Check your structure carefully at
> > that point.
> >
>
> Thank you for your response. I looked at the pdb file and atoms 803 and 804
> are O and H, respectively of a water molecule.
So: did you "check the structure carefully" in that region? Is there anything
special about that water? Have you visualized its interactions with the rest
of your system?
> When I
> looked at the system after the first equilibration, I found that protein
> moved out of the water box.
Please see the "autoimage" command in cpptraj: this will allow you to
visualize periodic systems in a more intuitive way. There is probably nothing
wrong with your system that is related to the protein moving out of the water
box.
....dac
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Received on Sun Jun 26 2016 - 11:00:04 PDT
