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.

Binod Nepal

Thank you!! Dr. LemKul. I will read the above link.