[AMBER] Seeking suggestions for breaking a covalent link between atoms

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Tue, 23 Mar 2021 14:24:59 +0530


I created a covalent bond between two carbons using the leap command
>bond mol.20.C mol.39.C
Then, the simulation was run for the protein having this covalent bond.

Now, I want to break this covalent bond and continue further with the
simulation. This time the start structure will be the last pdb of the
previous simulation but, without the covalent bond.

Can some suggest what to do to remove the covalent bond and continue the

Also, will the bond breaking require us to bring changes in the existing



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Received on Tue Mar 23 2021 - 02:00:02 PDT
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