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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Wed May 29 2019 - 12:30:02 PDT
