Re: [AMBER] protein domain "broken"

Date: Fri, 06 Nov 2020 12:20:18 +0100

Dear Anselm;

I rectify with my previous message, sorry. I have checked just that,
and indeed my disulfide bond was not defined, and that's why it
appeared broken in all dynamics. So my problem is summarized in: Even
not having put this bond in my input ... because in some cases one of
the two domains of the protein disappears? I am attaching two images
so you can see it better. I have opened the final molecule with
several programs and only one of two domains appears...

Thanks in advance,


"Dr. Anselm Horn" <> escribió:

> 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
> program.
> 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,
> Anselm
> 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 - 03:30:05 PST
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