Great thanks!!
On Wed, May 29, 2019, 22:10 Bill Ross <ross.cgl.ucsf.edu> wrote:
> Fabian,
>
> See the tutorials or manual to understand leaprc.
>
> This tutorial seems apt, searching 'the web' for loadpdbusingseq.
>
> Bill
>
>
> http://ambermd.org/tutorials/advanced/tutorial1/section4.htm
>
> polyATseq = {DA DA DA DA DA DA DA DA DA DA3 DT5 DT DT DT DT DT DT DT
> DT DT3 }
>
> Upon specifying the above sequence we will tell xleap to load our
> polyAT.pdb file but ignore the residue names in the pdb and instead use
> the sequence we have supplied.
>
> polyAT = loadpdbusingseq polyAT.pdb polyATseq
>
> Bill
>
>
> On 5/29/19 10:54 AM, Fabian Glaser wrote:
> > 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
> >>>
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> >>>
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Received on Wed May 29 2019 - 12:30:03 PDT
