Dear Bill
Thanks a lot for your answer.
I am not sure i follow your first idea, where i cand find the master config
and what i should do with it? I would be very happy to get some details. I will
check the script you mentioned.
Thanks a lot!
Fabian
AMBERSwipeMay 29, 2019, 17:12 Bill Ross <ross.cgl.ucsf.edu> wrote:
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 29 2019 - 11:00:02 PDT
