[AMBER] Intercalation site creation

From: Pooja Khurana <btpooja.yahoo.in>
Date: Tue, 5 Jul 2011 16:18:59 +0530 (IST)

Hi everyone,

I am working on the intercalators. And for my study purpose I need to computationally model the dna conformation having intercalation site. But having gone through several papers I found that different intercalators lead to different conformational changes in the dna. I can't come up with the consensus and getting confused on how to build the intercalation site. Can anyone suggest me a way to create the intercalation site independent of the nature of the intercalator? Or can I take any one intercalation site already in one of the crystal structure for creating the intercalation site and then do the minimization?

Waiting for an early reply.

Thanks in anticipation,
Pooja Khurana
NSIT Delhi.
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Received on Tue Jul 05 2011 - 04:00:03 PDT
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