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

From: Amit Sharma (Asstt. Prof., MCARS) <"Amit>
Date: Wed, 24 Mar 2021 19:58:11 +0530

Thanks for your help David,

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).
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."

Can you please help to figure out what might be going wrong.

To inform, I ran the following commands in parmed

>parm hmass.prmtop #Hmassrepartioned parameter file
>loadRestrt in.ncrst # loaded restart file from previous simulation with
>loadCoordinates # loaded nc file from previous simulation with bond
>deleteBond :20.C :39.C # delete bond between two specified atoms
>#HMassRepartition #
> writeCoordinates out.ncrst # write coordinates after bond deletion
> parmout hmass_delbond.prmtop # write parameter file after bond deletion


On Tue, Mar 23, 2021 at 7:14 PM David A Case <> wrote:

> 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

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Received on Wed Mar 24 2021 - 07:30:03 PDT
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