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,
Myriam
"Dr. Anselm Horn" <anselm.horn.fau.de> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
(image/jpeg attachment: smp-196ptn3.jpg)
(image/jpeg attachment: smp-196ptn4.jpg)
