[gmx-users] Simulation of Primed DNA-rtp entry and Terminal residue

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 6 15:32:47 CEST 2011

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Singh wrote:
> Hi  Justin,
> Thanks for quick response :)
> Basically I don't want terminal H atom.. instead of that I want O+ at 3' end
> and -CH2-O-PO3 at second. but it is appearing on both the ends... :(
> Any suggestions?

The suggestion is still the same and always will be - you need to create an .rtp 
entry that contains exactly what you want for the residue you need and perhaps 
an .hdb entry to go along with it.  It sounds like you haven't constructed that 
yet.  I don't know what O+ is in the context of DNA, so it's not clear to me 
what you're trying to do, especially since it sounds like you want two different 
3' ends.

I will also note that upon second glance through your D5TP .rtp entry, you don't 
actually have bonds between your P and O*P atoms, which I think you will find 
are quite necessary.



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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