[gmx-users] Adding modified nucleotide to a forcefield

william Stebbeds willstebbeds at hotmail.com
Thu Feb 3 21:55:21 CET 2011

I am attempting to add 8-oxo-dG (8-Oxo-2'-deoxyguanosine) to the amber99sb force field. This is a simple modification of the H8 hydrogen on a guanine to an oxygen atom. I have followed the instructions on the gromacs site on adding residues.
However the new nucleotide will not work, it will not attach to the adjacent nucleotides in the sequence.
Any help would be very much appreciated, if any more information is required please let me know.
Best Regards
William StebbedsCranfield UniversityUK
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