[AMBER] How to build a TT dimer

From: Shi Choong <shi.amber.linux.gmail.com>
Date: Wed, 23 Jun 2010 19:40:55 -0700


The structure I am doing now contains cyclobutane pyrimidine dimer (CPD)
lesion that is not available in xleap. So I plan to run the MD simulations
by replacing the CPD with TT dimer for now. However, there are 2 problems.
1) I don't see the coordinates for the CPD atoms on pdb file.
2) Does anyone know how to build a TT dimer?

By chance, is there an amber tutorial related to this type of structure that
has both DNA and protein?

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Received on Wed Jun 23 2010 - 20:00:04 PDT
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