removing a covalent bond during a simulation

From: patrick wintrode (
Date: Wed Jun 29 2005 - 12:10:56 CDT

Dear all,

I would like to simulate my protein for several
nanoseconds (basically until things are stable) and
then remove the peptide bond between two residues and
appropriately modify the residues (to make it as
though the bond was cleaved by a protease) - and then
continue the simulation.

Is there a way to accomplish this in the configuration

If not, can someone suggest the best way to proceed?
Taking the .coor file output by a simulation and
modifying it by hand would be easy enough, but then it
would no longer match the .vel file so it wouldn't be
possible to simply restart the simulations using those

Maybe I could improvise something using the alchemical
FEP capabilities?


Patrick L. Wintrode
Department of Physiology and Biophysics
Case Western Reserve University
Cleveland, Ohio 44106

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