The DA5 is due to the default residueNameList or similar - likely it is
set via your leaprc directly or indirectly. One way would be to make a
local copy of whatever master config does that, another more simple
would be to use loadPdbUsingSeq(uence?) assuming it still exists,
wherein you'd list all the residues just to force that one to be right.
Bill
On 5/29/19 7:04 AM, Fabian Glaser wrote:
> Hi,
>
> I am trying to process a protein-dna system through tleap (PDB 2xkk).
>
> Here, there is a PTR (phospho tyrosine) bound to the DNA through a C5’ atom of DA. Tleap works, but the problem is that instead of making a bond between C5’ and OP1, it treats the DA as a terminal DA5 and adds a O5’ (not present in the original pdb), which is wrong.
>
> How do I treat the PTR and DA to direct tleap to recognize the C5’ to OP1 bond?
>
> Thanks a lot,
> Fabian
>
>
>
> Best,
>
> Fabian
>
> Fabian Glaser PhD
>
> Head of the Structural Bioinformatics section
> Bioinformatics Knowledge Unit - BKU
> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology, Haifa, Israel
> Web http://bku.technion.ac.il/
> Tel +972 (0) 4 8293701
>
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Received on Wed May 29 2019 - 07:30:02 PDT
