On Wed, Oct 12, 2022, Jiaan Zhu wrote:
>
> Thanks for your suggestions! I checked the 1W5 and 1WA(another unnatural
> nucleotide) in the final pdb structure(generated by amb2pdb) and found it
> may due to the a O-O bond formed in the phosphate group of one 1WA. See
> below.
Note that when a graphics program draws a bond (or decides it is a single
vs. double bond) that has nothing to do with Amber. The pdb file doesn't
contain bond information, so visualization programs decide things based on
geometry and other heuristics.
> Info: There is a bond linking a non-head and non-tail residue atom (OP1)
> and an omitted atom (HOP1).
> You need to specifically add this bond in LEaP using the command
> 'bond <atom1> <atom2> [order]'
> to link OP1 to an atom in another residue (similar to disulfide
> bonds)!
Sounds like you need to just follow this advice (and hope it works!)
....dac
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Received on Fri Oct 14 2022 - 09:30:02 PDT
