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

[Tingguang.S]

Thank you Justin! I delete the phosphate group and the problem is resolved !


Best regards
Sting






From: Justin Lemkul <jalemkul at vt.edu>
Date: 2020-04-26 00:20:44
To:  gmx-users at gromacs.org
Subject: Re: [gmx-users] Why there is no phosphorous atom in the "DA5" residue in dna.rtp>
>
>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.
>Assistant Professor
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>Virginia Tech Department of Biochemistry
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