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Messages - dailiang

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MD simulations / generate DNA pdb file for Gromacs
« on: January 21, 2016, 07:55:22 pm »
The DNA pdb file generated by X3DNA has only A T C G, but no terminal base, e.g. A3, A5, T3, T5, ...
How to use X3DNA generate a pdb file with terminal bases?

The reason why I ask this question is because I am using X3DNA to generate initial DNA conformation for MD simulations by Gromacs.

In addition to the above question, is it possible to generate a pdb file that is fully compatible with Gromacs. Now there are some incompatible things. Such as Gromacs using DA, DT, DC, DG, rather than A, T, C, G.

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.