[gmx-users] pdb2gmx doesn´t generate H
Pascal Baumann
ehraboch at googlemail.com
Fri Jul 23 19:22:17 CEST 2010
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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