[gmx-users] Atom O5' not found in residue seq.nr. 1 while adding atom

[Justin A. Lemkul]

On 4/21/09 1:07 AM, mahr wrote:
> Dear Gromacs Users,
>
> I m trying to simulate a *DNA* structure with *amber03 force field*. However,
> when I give first command of pdb2gmx.
>
> Following error comes:
>
> *Fatal error:**Atom O5' not found in residue seq.nr. 1 while adding atom.*
>
> As O5’ is present in DA nucleic acid. So,I checked *DNA.rtp* file and
> nomenclature of DA, DT and all other nucleic acid residues is same for both .pdb
> and .rtp file.
>

The problem comes from the fact that this nucleic acid is at the 5' end of the 
molecule, thus the residue is not DA, but DA5, which has no phosphate group. 
Your molecule needs to conform to this expectation or else you will need to 
introduce parameters for a 5'-phosphorylated residue.

-Justin

> Plz plz guide me how to solve this problem.
>
> *Following is my .rtp file for DA*
>
> [ DA ]
>
> [ atoms ]
>
> P P 1.16590 1
>
> O1P O2 -0.77610 2
>
> O2P O2 -0.77610 3
>
> O5' OS -0.49540 4
>
> C5' CT -0.00690 5
>
> H5'1 H1 0.07540 6
>
> H5'2 H1 0.07540 7
>
> C4' CT 0.16290 8
>
> H4' H1 0.11760 9
>
> O4' OS -0.36910 10
>
> C1' CT 0.04310 11
>
> H1' H2 0.18380 12
>
> N9 N* -0.02680 13
>
> C8 CK 0.16070 14
>
> H8 H5 0.18770 15
>
> N7 NB -0.61750 16
>
> C5 CB 0.07250 17
>
> C6 CA 0.68970 18
>
> N6 N2 -0.91230 19
>
> H61 H 0.41670 20
>
> H62 H 0.41670 21
>
> N1 NC -0.76240 22
>
> C2 CQ 0.57160 23
>
> H2 H5 0.05980 24
>
> N3 NC -0.74170 25
>
> C4 CB 0.38000 26
>
> C3' CT 0.07130 27
>
> H3' H1 0.09850 28
>
> C2' CT -0.08540 29
>
> H2'1 HC 0.07180 30
>
> H2'2 HC 0.07180 31
>
> O3' OS -0.52320 32
>
> [ bonds ]
>
> P O1P
>
> P O2P
>
> P O5'
>
> O5' C5'
>
> C5' H5'1
>
> C5' H5'2
>
> C5' C4'
>
> C4' H4'
>
> C4' O4'
>
> C4' C3'
>
> O4' C1'
>
> C1' H1'
>
> C1' N9
>
> C1' C2'
>
> N9 C8
>
> N9 C4
>
> C8 H8
>
> C8 N7
>
> N7 C5
>
> C5 C6
>
> C5 C4
>
> C6 N6
>
> C6 N1
>
> N6 H61
>
> N6 H62
>
> N1 C2
>
> C2 H2
>
> C2 N3
>
> N3 C4
>
> C3' H3'
>
> C3' C2'
>
> C3' O3'
>
> C2' H2'1
>
> C2' H2'2
>
> -O3' P
>
> [ impropers ]
>
> C4 C8 N9 C1'
>
> C6 H61 N6 H62
>
> N9 N7 C8 H8
>
> N1 N3 C2 H2
>
> C5 N6 C6 N1
>
> *Following is DA part of my pdb file:*
>
> ATOM 28 P DA E 10 -24.026 32.156 -43.818 1.00180.08 P
>
> ATOM 29 O1P DA E 10 -23.715 31.139 -42.788 1.00173.83 O
>
> ATOM 30 O2P DA E 10 -25.435 32.499 -44.114 1.00161.01 O
>
> *ATOM 31 O5' DA E 10 -23.255 33.516 -43.475 1.00127.88 O*
>
> ATOM 32 C5' DA E 10 -23.498 34.194 -42.247 1.00107.59 C
>
> ATOM 33 C4' DA E 10 -23.169 33.299 -41.066 1.00102.86 C
>
> ATOM 34 O4' DA E 10 -21.825 32.777 -41.221 1.00 93.42 O
>
> ATOM 35 C3' DA E 10 -23.220 33.983 -39.705 1.00102.18 C
>
> ATOM 36 O3' DA E 10 -23.829 33.119 -38.754 1.00 83.31 O
>
> ATOM 37 C2' DA E 10 -21.755 34.244 -39.363 1.00102.50 C
>
> ATOM 38 C1' DA E 10 -21.012 33.153 -40.128 1.00 81.75 C
>
> ATOM 39 N9 DA E 10 -19.721 33.596 -40.647 1.00 82.20 N
>
> ATOM 40 C8 DA E 10 -19.495 34.603 -41.544 1.00 94.12 C
>
> ATOM 41 N7 DA E 10 -18.227 34.783 -41.832 1.00102.29 N
>
> ATOM 42 C5 DA E 10 -17.576 33.827 -41.070 1.00 96.10 C
>
> ATOM 43 C6 DA E 10 -16.215 33.496 -40.924 1.00 87.15 C
>
> ATOM 44 N6 DA E 10 -15.230 34.125 -41.572 1.00 84.12 N
>
> ATOM 45 N1 DA E 10 -15.903 32.488 -40.082 1.00 75.71 N
>
> ATOM 46 C2 DA E 10 -16.891 31.860 -39.434 1.00 80.51 C
>
> ATOM 47 N3 DA E 10 -18.203 32.081 -39.490 1.00 91.21 N
>
> ATOM 48 C4 DA E 10 -18.482 33.087 -40.334 1.00 96.39 C
>
> ATOM 49 H5'1 DA E 10 -22.876 35.088 -42.203 1.00105.06 H
>
> ATOM 50 H5'2 DA E 10 -24.549 34.479 -42.198 1.00105.06 H
>
> ATOM 51 H4' DA E 10 -23.867 32.462 -41.060 1.00105.06 H
>
> ATOM 52 H3' DA E 10 -23.768 34.923 -39.772 1.00105.06 H
>
> ATOM 53 H2'1 DA E 10 -21.447 35.234 -39.699 1.00105.06 H
>
> ATOM 54 H2'2 DA E 10 -21.583 34.154 -38.290 1.00105.06 H
>
> ATOM 55 H1' DA E 10 -20.863 32.292 -39.476 1.00105.06 H
>
> ATOM 56 H8 DA E 10 -20.295 35.202 -41.980 1.00105.06 H
>
> ATOM 57 H61 DA E 10 -15.458 34.926 -42.244 1.00105.06 H
>
> ATOM 58 H62 DA E 10 -14.214 33.827 -41.419 1.00105.06 H
>
> ATOM 59 H2 DA E 10 -16.579 31.056 -38.768 1.00105.06 H
>
> I will be very thankful.
>
> Best regards
>
> mahreen
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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