[gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp

[Justin Lemkul]

On 4/25/20 12:18 PM, Tingguang.S wrote:
> Dear all,
>
>
>     When I generated the amber99sb force filed topology of a DNA molecule with gmx, a error code appeared: "Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms". I tried to fix this but found there was no P atoms in all the 5' nucleic acid residues in dna.rtp.
>     Can some one help me with this ?

DNA is not typically phosphorylated on its 5'-hydroxyl. Synthetic 
nucleotides sometimes are, but the force field is designed for typical 
biologically relevant structures. If the 5'-phosphate is relevant (which 
it can be), you need to build your own .rtp entry or terminal database 
entry.

-Justin

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Justin A. Lemkul, Ph.D.
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jalemkul at vt.edu | (540) 231-3129
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