Hello!
Did you remove one of the oxygen (OP1 or OP2) atoms from the phosphate
group before making the bond?
Rodrigo
On Thu, Oct 12, 2023 at 5:58 AM Priyasha Majee via AMBER
<amber.ambermd.org> wrote:
>
>
>
> Dear All,
>
> I am working with a G-quadruplex system. I want to incorporate two
> modifications in the G-quadruplex sequence at 9 and 24 position as DF
> and BF respectively. When I first incorporated the modifications and ran
> MD simulatIon, in the production stage, the modification and the
> G-Quadruplex separated as if the modification is not a part of the
> system. Now, I am using 'bond' command to make covalent bonds between
> the atoms in the DNA backbone as follows :
>
> bond mol.8.O3' mol.9.P
>
> bond mol.9.O3' mol.10.P
>
> bond mol.23.O3' mol.24.P
>
> bond mol.24.O3' mol.25.P
>
> But after running this command, the g-quadruplex is splitting into
> multiple chains with TER before and after 9th and 24th modifications.
> Presence of TER is the end of one chain. So what might be causing this.
> Please provide insight and suggestions on how to correctify this.
>
> Thank you in advance
>
> Regards,
>
> Priyasha
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Received on Thu Oct 12 2023 - 09:00:02 PDT
