Hi. Can someone please help me.<div><br class="webkit-block-placeholder"></div><div>I am new to Gromacs. I have a 20mer DNA duplex I want to do some MD on. I start by making a topology file form the pdb file. When I run pdb2gmx and the amber99 force field I get this fatal error:<div>
'Atom 02 in residue DT 3 not found in rtp entry with 32 atoms while sorting atoms'</div><div><br class="webkit-block-placeholder"></div><div>Here is the portion of the pdb file containing the atom in question:</div>
<div><div>ATOM 37 C4 DA A 2 2.705 -1.868 3.118 1.00 0.00 </div><div>ATOM 38 C3' DA A 2 6.858 -4.420 2.715 1.00 0.00 </div><div>ATOM 39 C2' DA A 2 5.664 -4.141 3.627 1.00 0.00 </div>
<div>ATOM 40 O3' DA A 2 7.933 -3.562 3.073 1.00 0.00 </div><div>ATOM 41 P DT A 3 8.308 -3.390 4.619 1.00 0.00 </div><div><span class="Apple-style-span" style="font-weight: bold;">ATOM 42 O1P DT A 3 9.773 -3.228 4.760 1.00 0.00</span> </div>
<div>ATOM 43 O2P DT A 3 7.705 -4.493 5.401 1.00 0.00 </div><div>ATOM 44 O5' DT A 3 7.575 -2.013 4.972 1.00 0.00 </div><div>ATOM 45 C5' DT A 3 7.588 -0.948 4.004 1.00 0.00 </div>
<div><br class="webkit-block-placeholder"></div><div>Where atom 02 must be O1P in DT 3</div><div><br class="webkit-block-placeholder"></div><div>Here is the portion of the amber99 .rtf file for the DT nucleotide:</div><div>
<div>[ DT ]</div><div> [ atoms ]</div><div> P amber99_46 1.16590 1</div><div> O1P amber99_45 -0.77610 2</div><div> O2P amber99_45 -0.77610 3</div><div> O5' amber99_44 -0.49540 4</div>
<div> C5' amber99_11 -0.00690 5</div><div> H5'1 amber99_19 0.07540 6</div><div> H5'2 amber99_19 0.07540 7</div><div> C4' amber99_11 0.16290 8</div><div> H4' amber99_19 0.11760 9</div>
<div> O4' amber99_44 -0.36910 10</div><div> C1' amber99_11 0.06800 11</div><div> H1' amber99_20 0.18040 12</div><div> N1 amber99_40 -0.02390 13</div><div> C6 amber99_7 -0.22090 14</div>
<div> H6 amber99_23 0.26070 15</div><div> C5 amber99_7 0.00250 16</div><div> C7 amber99_11 -0.22690 17</div><div> H71 amber99_18 0.07700 18</div><div> H72 amber99_18 0.07700 19</div>
<div> H73 amber99_18 0.07700 20</div><div> C4 amber99_2 0.51940 21</div><div> O4 amber99_41 -0.55630 22</div><div> N3 amber99_35 -0.43400 23</div><div> H3 amber99_17 0.34200 24</div>
<div> C2 amber99_2 0.56770 25</div><div> O amber99_41 -0.58810 26</div><div> C3' amber99_11 0.07130 27</div><div> H3' amber99_19 0.09850 28</div><div> C2' amber99_11 -0.08540 29</div>
<div> H2'1 amber99_18 0.07180 30</div><div> H2'2 amber99_18 0.07180 31</div><div> O3' amber99_44 -0.52320 32</div><div><br class="webkit-block-placeholder"></div><div>I can't see why atom 02 shouldn't be found.</div>
<div><br class="webkit-block-placeholder"></div><div>I am running GROMACS 4.0.5 on Mac OS 10.5</div><div><br class="webkit-block-placeholder"></div><div>Thanks,</div><div>Gunnar W.</div><div><br class="webkit-block-placeholder">
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