Re: [gmx-users] pdb2gmx doesn´t generate H
Oliver Grant
olymacfoogal at gmail.com
Sat Jul 24 19:23:48 CEST 2010
Hi,
This seems to be a problem with amber ports in gromacs. I believe it is
because the residue attached to an N terminal residue. Try manually adding
the hydrogen to the backbone nitrogen in the SER2 in the pdb. This solved
the problem for me although there were reports from other people of the
problem then moving to the 3rd residue. Please post what you find works for
you.
Oliver
On 23 July 2010 18:22, Pascal Baumann <ehraboch at googlemail.com> wrote:
> 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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