SMD on membrane protein.

From: Yoav Beck (ucbpybe_at_ucl.ac.uk)
Date: Sun Aug 23 2009 - 09:04:55 CDT

Dear all,

I have a membrane protein (beta barrel) with a plug. I am trying to
exert constant force on the plug.
I followed the tutorial, but I declared all the plug's atoms as the smd
atoms, and exert the force perpendicularly to the membrane (x=y=0, z=1).
I tried with no fixed atoms, and with the membrane fixed. The outcome is
always the same:
Constraint failure in RATTLE algorithm for atom 85977!
Note that it is not always the same atom which cause a problem, but it
is always one on the plug.

//Any suggestions would be of great help.

Thanks,

Yoav.

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