Hello Catherine!
I am doing the same kind of study for my PhD work so maybe my experience can
help you.
What I do is generate the DNA pdb chain with nucgen and run it through tleap
once so it gets all fixed up. With its parmtop and coordinate files I
generate a DNA_corrected pdb and open it in DS Visualizer (or any pdb
viewer). I then import my ligand and manually place it between the base
pair of my interest. Save the pdb and open it into tleap to generate the
parmtop and crd file for simulation. If your ligand does not have any
unusual residues, this idea should work flawlessly for you.
Hope it helps and if I can help any further, let me know!
Have a great week,
Rodrigo.
-----------------------------------
PhD Student
Depto de Fisicoquímica
Instituto de Química
Universidad Nacional Autónoma de México
2010/7/5 Catein Catherine <askamber23.hotmail.com>
>
> Dear All,
>
>
>
> I have to study a drug bind to a 18 base pairs DNA. The drug intercalated
> to the 9th residues by cleaving one of the strands of the DNA as follows:
> (pls forgive me about the base-pair rules, this sequence is just design for
> illustration purposes, ^ indicate the intercalation site). Here is the
> seqeuence:
>
>
>
> AAAAAAAAG^TAAAAAAAA
>
> AAAAAAAAAAAAAAAAAA
>
>
>
> I think there are two ways to define this double strand DNA
>
>
>
> (I)
>
>
>
> DA3DADADADADADADA DG^DT DADADADADADADADADA5
>
> DA5DADADADADADADADADADADADADADADADADADA3
>
>
>
> (II)
>
>
>
> DA3DADADADADADADA DG5^DT3 DADADADADADADADADA5
>
> DA5DADADADADADADADADADADADADADADADADADA3
>
>
>
> Pls noted that the cleavage site was defined as DG5^DT3 in the (II) case,
> while DG^DT was used in the (I) case.
>
>
>
> I want to ask for your professional advice which one is correct in theory.
>
>
>
> In any case, if I really need to use DG^DT instead of the terminal
> residues. how can I make the correction in xleap?
>
> I found xleap automatically change DG^DT to DG5^DT3 even if I removed the
> ter card between DG and DT in the pdb file, and even if I use the DG/DT as
> the name of the residue in the pdb file.
>
>
>
> I understand I maybe able to use clearrespdbmap to stop ALL automation
> process in xleap. However, I don't want to do this, as I still believe
> xleap are good at locating errors and added missing atoms for the rest of
> the residues, which I need this automatic function, I just want to make a
> specific changes to one or two residues intentionally. Are there any way to
> do so?
>
>
>
> Many thanks in advance for your help and guidances.
>
>
>
> Best regards,
>
>
>
> Catherine
>
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Received on Mon Jul 05 2010 - 06:30:04 PDT
