Hi<br><br>I´m using GROMACS 4.0.7 with the Amber99sb forcefield.<br><br>I keep getting an error when I´m typing this command:<br>pdb2gmx -f t.pdb -o t2.pdb -ff amber99sb -water tip3p<br><br>I get this message:<br><br>WARNING: atom H is missing in residue SER 2 in the pdb file<br>
You might need to add atom H to the hydrogen database of residue SER<br> in the file ff???.hdb (see the manual)<br><br>Here are the corresponding lines of the files:<br><br>reductase.pdb:<br><br>ATOM 1 N NSE A 1 14.028 -45.099 41.393 1.00 70.61 N<br>
ATOM 2 CA NSE A 1 13.637 -45.030 39.942 1.00 69.85 C<br>ATOM 3 C NSE A 1 12.332 -44.253 39.785 1.00 66.00 C<br>ATOM 4 O NSE A 1 11.291 -44.680 40.290 1.00 67.41 O<br>
ATOM 5 CB NSE A 1 13.473 -46.443 39.354 1.00 73.80 C<br>ATOM 6 OG NSE A 1 12.142 -46.925 39.510 1.00 75.14 O<br>ATOM 7 N SER A 2 12.366 -43.138 39.069 1.00 61.51 N<br>
ATOM 8 CA SER A 2 11.249 -42.208 39.122 1.00 57.44 C<br>ATOM 9 C SER A 2 10.277 -42.342 37.951 1.00 56.07 C<br>ATOM 10 O SER A 2 10.692 -42.367 36.799 1.00 55.81 O<br>
ATOM 11 CB SER A 2 11.785 -40.789 39.233 1.00 54.79 C<br>ATOM 12 OG SER A 2 12.679 -40.695 40.327 1.00 54.65 O<br>ATOM 13 N VAL A 3 8.984 -42.423 38.280 1.00 54.68 N<br>
ATOM 14 CA VAL A 3 7.904 -42.613 37.311 1.00 54.35 C<br>ATOM 15 C VAL A 3 6.728 -41.642 37.550 1.00 51.88 C<br>ATOM 16 O VAL A 3 5.964 -41.802 38.500 1.00 52.51 O<br>
ATOM 17 CB VAL A 3 7.359 -44.074 37.341 1.00 57.72 C<br>ATOM 18 CG1 VAL A 3 6.311 -44.289 36.237 1.00 57.58 C<br>ATOM 19 CG2 VAL A 3 8.498 -45.108 37.236 1.00 59.10 C<br>
<br>ffamber99sb.rtp:<br><br> <br>[ SER ]<br> [ atoms ]<br> N amber99_34 -0.41570 1<br> H amber99_17 0.27190 2<br> CA amber99_11 -0.02490 3<br> HA amber99_19 0.08430 4<br>
CB amber99_11 0.21170 5<br> HB1 amber99_19 0.03520 6<br> HB2 amber99_19 0.03520 7<br> OG amber99_43 -0.65460 8<br> HG amber99_25 0.42750 9<br> C amber99_2 0.59730 10<br>
O amber99_41 -0.56790 11<br> [ bonds ]<br> N H<br> N CA<br> CA HA<br> CA CB<br> CA C<br> CB HB1<br> CB HB2<br> CB OG<br> OG HG<br> C O<br> -C N<br>
[ dihedrals ]<br> CA C +N +H backbone_prop_1<br> O C +N +H backbone_prop_2<br> -C N CA CB backbone_prop_3<br> -C N CA C backbone_prop_4<br> CA C +N +CA backbone_prop_1<br>
O C +N +CA backbone_prop_1<br> [ impropers ]<br> -C CA N H<br> CA +N C O<br> <br> <br>ffamber99sb.hdb:<br><br>SER 4<br>1 1 H N -C CA <br>
1 5 HA CA N CB C <br>2 6 HB CB CA OG <br>1 2 HG OG CB CA <br><br>When I´m running the command with -missing I get a topol.top file, where just the SER 2 is missing the H. The other SER work properly.<br>
Here are some lines:<br><br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 amber99_39 1 NSE N 1 0.1849 14.01 ; qtot 0.1849<br>
2 amber99_17 1 NSE H1 2 0.1898 1.008 ; qtot 0.3747<br> 3 amber99_17 1 NSE H2 3 0.1898 1.008 ; qtot 0.5645<br> 4 amber99_17 1 NSE H3 4 0.1898 1.008 ; qtot 0.7543<br>
5 amber99_11 1 NSE CA 5 0.0567 12.01 ; qtot 0.811<br> 6 amber99_28 1 NSE HA 6 0.0782 1.008 ; qtot 0.8892<br> 7 amber99_11 1 NSE CB 7 0.2596 12.01 ; qtot 1.149<br>
8 amber99_19 1 NSE HB1 8 0.0273 1.008 ; qtot 1.176<br> 9 amber99_19 1 NSE HB2 9 0.0273 1.008 ; qtot 1.203<br> 10 amber99_43 1 NSE OG 10 -0.6714 16 ; qtot 0.532<br>
11 amber99_25 1 NSE HG 11 0.4239 1.008 ; qtot 0.9559<br> 12 amber99_2 1 NSE C 12 0.6163 12.01 ; qtot 1.572<br> 13 amber99_41 1 NSE O 13 -0.5722 16 ; qtot 1<br>
14 amber99_34 2 SER N 14 -0.4157 14.01 ; qtot 0.5843<br> 15 amber99_11 2 SER CA 15 -0.0249 12.01 ; qtot 0.5594<br> 16 amber99_19 2 SER HA 16 0.0843 1.008 ; qtot 0.6437<br>
17 amber99_11 2 SER CB 17 0.2117 12.01 ; qtot 0.8554<br> 18 amber99_19 2 SER HB1 18 0.0352 1.008 ; qtot 0.8906<br> 19 amber99_19 2 SER HB2 19 0.0352 1.008 ; qtot 0.9258<br>
20 amber99_43 2 SER OG 20 -0.6546 16 ; qtot 0.2712<br> 21 amber99_25 2 SER HG 21 0.4275 1.008 ; qtot 0.6987<br> 22 amber99_2 2 SER C 22 0.5973 12.01 ; qtot 1.296<br>
23 amber99_41 2 SER O 23 -0.5679 16 ; qtot 0.7281<br><br> 207 amber99_34 16 SER N 207 -0.4157 14.01 ; qtot 0.3124<br> 208 amber99_17 16 SER H 208 0.2719 1.008 ; qtot 0.5843<br>
209 amber99_11 16 SER CA 209 -0.0249 12.01 ; qtot 0.5594<br> 210 amber99_19 16 SER HA 210 0.0843 1.008 ; qtot 0.6437<br> 211 amber99_11 16 SER CB 211 0.2117 12.01 ; qtot 0.8554<br>
212 amber99_19 16 SER HB1 212 0.0352 1.008 ; qtot 0.8906<br> 213 amber99_19 16 SER HB2 213 0.0352 1.008 ; qtot 0.9258<br> 214 amber99_43 16 SER OG 214 -0.6546 16 ; qtot 0.2712<br>
215 amber99_25 16 SER HG 215 0.4275 1.008 ; qtot 0.6987<br> 216 amber99_2 16 SER C 216 0.5973 12.01 ; qtot 1.296<br> 217 amber99_41 16 SER O 217 -0.5679 16 ; qtot 0.7281<br>
<br> 3489 amber99_34 226 SER N 3489 -0.4157 14.01 ; qtot -15.69<br> 3490 amber99_17 226 SER H 3490 0.2719 1.008 ; qtot -15.42<br> 3491 amber99_11 226 SER CA 3491 -0.0249 12.01 ; qtot -15.44<br>
3492 amber99_19 226 SER HA 3492 0.0843 1.008 ; qtot -15.36<br> 3493 amber99_11 226 SER CB 3493 0.2117 12.01 ; qtot -15.14<br> 3494 amber99_19 226 SER HB1 3494 0.0352 1.008 ; qtot -15.11<br>
3495 amber99_19 226 SER HB2 3495 0.0352 1.008 ; qtot -15.07<br> 3496 amber99_43 226 SER OG 3496 -0.6546 16 ; qtot -15.73<br> 3497 amber99_25 226 SER HG 3497 0.4275 1.008 ; qtot -15.3<br>
3498 amber99_2 226 SER C 3498 0.5973 12.01 ; qtot -14.7<br> 3499 amber99_41 226 SER O 3499 -0.5679 16 ; qtot -15.27<br> <br>-KHS<br>