The program you used to create the structure is changing the atom
names of the phosphate in the terminal region.
Created a new atom named: P within residue: .R<DC5 1>
Created a new atom named: O1P within residue: .R<DC5 1>
Created a new atom named: O2P within residue: .R<DC5 1>
Created a new atom named: P within residue: .R<DA5 11>
Created a new atom named: O1P within residue: .R<DA5 11>
Created a new atom named: O2P within residue: .R<DA5 11>
Just delete those atoms in your PDB. LeAP will add the correct atoms.
I tried it and it worked.
Hope that helps!
Rodrigo.
On Wed, Aug 17, 2022 at 10:21 AM Sneha Kandapal via AMBER
<amber.ambermd.org> wrote:
>
> Hello Team,
>
> I am new to AMBER and following the tutorial on the website. I am trying to minimize a DNA structure for which I followed the tutorial on the website.
>
> For my DNA structure I generated an intercalation cavity. When I am trying to load the system, it says "the file contained 6 atoms not in residue templates". Can somebody please help me understand how I can solve this issue. I am also attaching my pdb file here.
>
> Thank you for your help.
>
> Regards,
> Sneha
>
>
>
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Received on Wed Aug 17 2022 - 10:00:06 PDT