[AMBER] phosphor tyrosine bound to C5' terminal DA5

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Wed, 29 May 2019 17:04:19 +0300


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 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 - 07:30:03 PDT
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