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

From: David A Case <>
Date: Wed, 24 Mar 2021 11:17:49 -0400

On Wed, Mar 24, 2021, Amit Sharma (Asstt. Prof., MCARS) wrote:

>I tried deleteBond in parmed, but the output coordinate file (out.ncrst or
>out.pdb) still shows the bond (when seen in vmd or pymol).

If you just give a pdb file to a graphics program, it has to try to figure
out what bonds are there, just based on distance. Since your two carbon
atoms are still at bonding distance (parmed doesn't change the coordinates)
a bond will be shown visually.

You can print bonds in ParmEd to verify the bond is missing. You can also
load the prmtop and coordinate files in VMD, and it will show just bonds
that are actually there.

>But, I still continued further with the simulation using new prmtop file
>(hmass_delbond.prmtop). Here, if I run using pmemd.cuda, pmemd terminates
>abnormally and if I use sander the log file says
>"Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 1 390 777 778
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system."

This is to be expected: your two carbon atoms are now treated as non-bonded,
yet they are way too close for that, and you will have very large initial
forces and energy. You will need to minimize the system (use a CPU) before
continuing with MD.

But be sure this is really what you want to do: as I said before, just
removing a bond leaves you with a system that doesn't make any chemical
sense. Be sure you understand what you hope to learn from such a


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Received on Wed Mar 24 2021 - 08:30:03 PDT
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