How to get the topology file for the alkylated or modified DNA?

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fatal error

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fatal error

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fatal error

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fatal error

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Justin Lemkul

You have to parametrize the new residue.

http://www.gromacs.org/Documentation/How-tos/Parameterization

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Adding an alkyl substituent should be fairly straightforward, but there will be charge calculations to carry out as well as some new bonded parameters.