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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.
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.