Re: [AMBER] protein domain "broken"

Date: Fri, 06 Nov 2020 12:21:48 +0100

Hi Bill,

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,


Bill Ross <> escribió:

> Normally bonds that seem to disappear were not made in the first place.
> Bill
> On 11/6/20 2:45 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 - 03:30:06 PST
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