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

From: David A Case <>
Date: Tue, 23 Mar 2021 09:40:29 -0400

On Tue, Mar 23, 2021, Amit Sharma (Asstt. Prof., MCARS) wrote:
>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.

The "deleteBond" action in ParmEd will let you create a new prmtop file
without the bond you want to delete. Then you could just continue the
simulation from the last restart file.

However, if you just delete a C--C bond, you will have nonsensical
chemistry, at least from a molecular mechanics standpoint, since each of the
two carbons will now have an open valence. So it seems likely that you will
have to add bonds as well. In that case, you would need to hand-edit the
PDB file to represent the new chemistry, then re-run tleap to make the new
prmtop file.

...hope this helps...dac

AMBER mailing list
Received on Tue Mar 23 2021 - 07:00:03 PDT
Custom Search