[gmx-users] Adding modified nucleotide to a forcefield

[Justin A. Lemkul]

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.

-Justin

> Best Regards
> 
> William Stebbeds
> Cranfield University
> UK
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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