Thank you Justin! I delete the phosphate group and the problem is resolved !
From: Justin Lemkul
Date: 2020-04-26 00:20:44
Subject: Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue
>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
>Justin A. Lemkul, Ph.D.
>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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