Hello,
The only modification I'd make is to use nab instead of nucgen to generate
the PDB file for the nucleic acid. See the tutorial Basic 1 I believe (
ambermd.org/tutorials/basic/tutorial1). I'm not exactly sure, since the
website is acting up. However, nab will create a PDB that conforms to the
current standard and creates files that can be directly read into tleap
without modification.
Good luck!
Jason
On Mon, Jul 5, 2010 at 9:27 AM, ros <ros.servidor.unam.mx> wrote:
> 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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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jul 05 2010 - 07:30:03 PDT
