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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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