TclForces and wrapping

From: Gianluca Interlandi (
Date: Wed Aug 13 2008 - 03:05:43 CDT

I'm performing a simulation with a protein bound to mannose. I'm applying
TclForces to harmonically constrain the distance between the center of
mass of mannose and one atom of the protein.

I have "wrapall on". What happens if the protein gets wrapped around but
mannose does not, or vice versa? "loadcoords" loads the
current coordinates of the atoms involved in the calculation of the
forces. But does "loadcoords" take into account that one of the two
molecules might have been wrapped around? Is it wise to turn off



Gianluca Interlandi, PhD
                     +1 (206) 685 4435
                     +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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