[gmx-users] Adding modified nucleotide to a forcefield

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 3 22:07:42 CET 2011

william Stebbeds wrote:
> Hello,
> 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.

So a bond is missing?

> Any help would be very much appreciated, if any more information is 
> required please let me know.

A lot more information is needed, at the very least, your .rtp entry.


> Best Regards
> William Stebbeds
> Cranfield University
> UK


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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