[AMBER] Should I define drug intercalation site of a DNA as internal (DT/DA) or terminal (DT3/DA5) unit ?

From: Catein Catherine <askamber23.hotmail.com>
Date: Mon, 5 Jul 2010 17:59:23 +0800

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:





I think there are two ways to define this double strand DNA












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,


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Received on Mon Jul 05 2010 - 03:00:05 PDT
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