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