[gmx-users] pdb2gmx doesn´t generate H
Justin A. Lemkul
jalemkul at vt.edu
Mon Jul 26 01:14:05 CEST 2010
Oliver Grant wrote:
> 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.
>
I would also suggest using proper names in the input file. I don't know how
"NSE" is even working, when it should be "NSER." Syntactically correct input
files shouldn't generate these errors (at least, they never have in my experience).
-Justin
> Oliver
>
> On 23 July 2010 18:22, Pascal Baumann <ehraboch at googlemail.com
> <mailto: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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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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