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 <[email protected]
<mailto:[email protected]>> 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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