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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Office: 301 Fralin Hall
Lab: 303 Engel Hall
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