Re: [AMBER] protein domain "broken"

From: Dr. Anselm Horn <>
Date: Fri, 6 Nov 2020 12:03:22 +0100

Dear Myriam,

I'm not sure that I understood your problem correctly:
If the issue is a non-existent disulfide bond, how do you know that it
is broken?

If you just see no bond in your visualization program that might just be
a problem of cutoffs for bond assumption and thus visualization in that

If you see in your simulation that the distance between the two SG atoms
of the CYX residues increases to values well above the intial value,
then the disulfide bond might be absent.

You could check your topology file with the parmed tool.
Use the printBonds command to print all bonds involving SG atoms; if the
disulfide bond is not present, it was not present in the beginning.

Maybe that helps.

All the best,


On 11/06/2020 11:45 AM, MYRIAN TORRES RICO wrote:
> Dear all,
> I wanted to take a query about some results that I have obtained in my
> molecular dynamics.
> I have launched a dynamic of a protein-ligand complex (the ligand is a
> tretasaccharide), and of the two domains that the pdb of my protein
> initially presents, the disulfide bonds that form one of them ends up
> breaking ... But the energy data endings are the same as in any other
> dynamic that has been launched under the same conditions and with the
> same complex ...
> Has someone this or something similar happened to him?
> any ideas?
> Thanks in advance,
> Myriam
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Received on Fri Nov 06 2020 - 03:30:03 PST
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