[gmx-users] Capping (neuralising) of peptide
Nuno R. L. Ferreira
nunolf at ci.uc.pt
Thu Sep 30 15:14:12 CEST 2004
Alok
You are gettting 16 residues because you have chunks of 4 residues (between
TER tags) repeated 4 times (till END tag). The fourth residue is in the
C-terminal (GLY 2 in your pdb).
My guess is that is played around with insight, but forgot to delete
previous molecules created.
Create your tripeptite , and as David implicitely said, do not worry about
the terminals, cause you can cap them under pdb2gmx.
----- Original Message -----
From: "Alok" <alokjain at iitk.ac.in>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, September 30, 2004 1:54 PM
Subject: Re: [gmx-users] Capping (neuralising) of peptide
Hello
Thanks for your suggestion.
i used that options but now i am getting following Fatal error.
i used pdb2gmx -ignh -ter -f peptide.pdb -o peptide.gro -p peptide.top
Opening library file /usr/local/share/gromacs/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 Forcefield (official distribution)
1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
4: Gromacs Forcefield (see manual)
5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)
0
Looking whether force field file ffG43a1.rtp exists
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Reading peptide.pdb...
Read 64 atoms
Opening library file /usr/local/share/gromacs/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 16 residues with 64 atoms
chain #res #atoms
1 ' ' 16 64
WARNING: there were 1 atoms with zero occupancy and 0 atoms with
occupancy unequal to one (out of 64 atoms). Check your pdb file.
Opening library file /usr/local/share/gromacs/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file /usr/local/share/gromacs/top/ffG43a1.rtp
Residue 96
Sorting it all out...
Opening library file /usr/local/share/gromacs/top/ffG43a1.hdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-n.tdb
Opening library file /usr/local/share/gromacs/top/ffG43a1-c.tdb
Back Off! I just backed up peptide.top to ./#peptide.top.16#
Processing chain 1 (64 atoms, 16 residues)
Opening library file /usr/local/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 12 donors and 16 acceptors
There are 19 hydrogen bonds
Checking for duplicate atoms....
Select N-terminus type (start)
0: GLY-NH3+
1: NH2
2: None
1
N-terminus: NH2
Select C-terminus type (end)
0: COO-
1: COOH
2: None
1
C-terminus: COOH
Fatal error: Atom C not found in residue GLY16 while adding hydrogens
My PDB file :-
ATOM 1 N GLY 1 15.055 26.899 27.745 1.00 0.00
N
ATOM 2 CA GLY 1 14.262 27.999 27.204 1.00 0.00
C
ATOM 3 C GLY 1 14.753 29.328 27.725 1.00 0.00
C
ATOM 4 O GLY 1 15.669 29.411 28.537 1.00 0.00
O
ATOM 5 1H GLY 1 15.783 27.276 28.371 1.00 0.00
H
ATOM 6 2H GLY 1 14.444 26.262 28.276 1.00 0.00
H
ATOM 7 1HA GLY 1 14.313 28.000 26.100 1.00 0.00
H
ATOM 8 2HA GLY 1 13.198 27.873 27.476 1.00 0.00
H
ATOM 9 N PRO 1B 14.138 30.394 27.257 1.00 0.00
N
ATOM 10 CA PRO 1B 14.502 31.745 27.655 1.00 0.00
C
ATOM 11 C PRO 1B 14.016 32.068 29.078 1.00 0.00
C
ATOM 12 O PRO 1B 12.967 31.584 29.504 1.00 0.00
O
ATOM 13 CB PRO 1B 13.737 32.594 26.628 1.00 0.00
C
ATOM 14 CG PRO 1B 12.506 31.737 26.294 1.00 0.00
C
ATOM 15 CD PRO 1B 13.059 30.311 26.295 1.00 0.00
C
ATOM 16 HA PRO 1B 15.585 31.876 27.616 1.00 0.00
H
ATOM 17 1HB PRO 1B 13.474 33.584 27.007 1.00 0.00
H
ATOM 18 2HB PRO 1B 14.352 32.706 25.731 1.00 0.00
H
ATOM 19 1HG PRO 1B 11.763 31.839 27.088 1.00 0.00
H
ATOM 20 2HG PRO 1B 12.057 32.005 25.335 1.00 0.00
H
ATOM 21 1HD PRO 1B 12.312 29.578 26.607 1.00 0.00
H
ATOM 22 2HD PRO 1B 13.464 30.046 25.315 1.00 0.00
H
ATOM 23 N GLY 1C 14.726 32.860 29.852 1.00 0.00
N
ATOM 24 CA GLY 1C 14.238 33.314 31.151 1.00 0.00
C
ATOM 25 C GLY 1C 13.769 34.748 31.082 1.00 0.00
C
ATOM 26 O GLY 1C 13.445 35.378 32.087 1.00 0.00
O
ATOM 27 H GLY 1C 15.654 33.172 29.532 1.00 0.00
H
ATOM 28 1HA GLY 1C 13.403 32.675 31.489 1.00 0.00
H
ATOM 29 2HA GLY 1C 15.036 33.230 31.910 1.00 0.00
H
ATOM 30 O GLY 2 13.704 35.373 29.853 1.00 0.00
O
ATOM 31 HO GLY 2 13.391 36.273 29.966 1.00 0.00
H
TER
ATOM 32 N GLY 1 56.800 33.657 40.211 1.00 0.00
N
ATOM 33 CA GLY 1 55.946 34.770 39.811 1.00 0.00
C
ATOM 34 C GLY 1 56.520 36.088 40.276 1.00 0.00
C
ATOM 35 O GLY 1 57.546 36.150 40.944 1.00 0.00
O
ATOM 36 1H GLY 1 57.615 34.017 40.728 1.00 0.00
H
ATOM 37 2H GLY 1 56.269 33.014 40.815 1.00 0.00
H
ATOM 38 1HA GLY 1 55.833 34.791 38.711 1.00 0.00
H
ATOM 39 2HA GLY 1 54.932 34.647 40.234 1.00 0.00
H
ATOM 40 N PRO 1B 55.851 37.165 39.921 1.00 0.00
N
ATOM 41 CA PRO 1B 56.282 38.506 40.283 1.00 0.00
C
ATOM 42 C PRO 1B 56.014 38.808 41.767 1.00 0.00
C
ATOM 43 O PRO 1B 55.036 38.322 42.335 1.00 0.00
O
ATOM 44 CB PRO 1B 55.382 39.378 39.395 1.00 0.00
C
ATOM 45 CG PRO 1B 54.108 38.535 39.232 1.00 0.00
C
ATOM 46 CD PRO 1B 54.642 37.105 39.127 1.00 0.00
C
ATOM 47 HA PRO 1B 57.349 38.632 40.087 1.00 0.00
H
ATOM 48 1HB PRO 1B 55.187 40.363 39.824 1.00 0.00
H
ATOM 49 2HB PRO 1B 55.859 39.502 38.419 1.00 0.00
H
ATOM 50 1HG PRO 1B 53.490 38.628 40.128 1.00 0.00
H
ATOM 51 2HG PRO 1B 53.524 38.823 38.355 1.00 0.00
H
ATOM 52 1HD PRO 1B 53.942 36.372 39.534 1.00 0.00
H
ATOM 53 2HD PRO 1B 54.896 36.856 38.094 1.00 0.00
H
ATOM 54 N GLY 1C 56.838 39.581 42.441 1.00 0.00
N
ATOM 55 CA GLY 1C 56.550 40.015 43.806 1.00 0.00
C
ATOM 56 C GLY 1C 56.089 41.453 43.830 1.00 0.00
C
ATOM 57 O GLY 1C 55.923 42.068 44.883 1.00 0.00
O
ATOM 58 H GLY 1C 57.711 39.892 41.993 1.00 0.00
H
ATOM 59 1HA GLY 1C 55.769 39.375 44.253 1.00 0.00
H
ATOM 60 2HA GLY 1C 57.451 39.913 44.437 1.00 0.00
H
TER
ATOM 61 O GLY 2 55.849 42.100 42.635 1.00 0.00
O
ATOM 62 HO GLY 2 55.564 43.000 42.808 1.00 0.00
H
ATOM 63 N GLY 1 51.433 80.760 35.677 1.00 0.00
N
ATOM 64 CA GLY 1 50.640 81.859 35.136 1.00 0.00
C
ATOM 65 C GLY 1 51.130 83.189 35.657 1.00 0.00
C
ATOM 66 O GLY 1 52.047 83.271 36.469 1.00 0.00
O
ATOM 67 1H GLY 1 52.160 81.136 36.303 1.00 0.00
H
ATOM 68 2H GLY 1 50.822 80.123 36.208 1.00 0.00
H
ATOM 69 H GLY 1 50.690 81.860 34.032 1.00 0.00
H
ATOM 70 2HA GLY 1 49.575 81.733 35.408 1.00 0.00
H
ATOM 71 N PRO 1B 50.515 84.254 35.189 1.00 0.00
N
ATOM 72 CA PRO 1B 50.880 85.605 35.587 1.00 0.00
C
ATOM 73 C PRO 1B 50.393 85.929 37.009 1.00 0.00
C
ATOM 74 O PRO 1B 49.345 85.444 37.436 1.00 0.00
O
ATOM 75 CB PRO 1B 50.115 86.454 34.560 1.00 0.00
C
ATOM 76 CG PRO 1B 48.884 85.597 34.226 1.00 0.00
C
ATOM 77 CD PRO 1B 49.437 84.171 34.227 1.00 0.00
C
ATOM 78 HA PRO 1B 51.963 85.737 35.548 1.00 0.00
H
ATOM 79 1HB PRO 1B 49.852 87.444 34.939 1.00 0.00
H
ATOM 80 2HB PRO 1B 50.730 86.566 33.663 1.00 0.00
H
ATOM 81 1HG PRO 1B 48.140 85.700 35.020 1.00 0.00
H
ATOM 82 2HG PRO 1B 48.434 85.866 33.267 1.00 0.00
H
ATOM 83 1HD PRO 1B 48.689 83.438 34.538 1.00 0.00
H
ATOM 84 2HD PRO 1B 49.841 83.907 33.247 1.00 0.00
H
ATOM 85 N GLY 1C 51.104 86.721 37.784 1.00 0.00
N
ATOM 86 CA GLY 1C 50.615 87.174 39.083 1.00 0.00
C
ATOM 87 C GLY 1C 50.147 88.609 39.014 1.00 0.00
C
ATOM 88 O GLY 1C 49.823 89.239 40.019 1.00 0.00
O
ATOM 89 H GLY 1C 52.032 87.032 37.464 1.00 0.00
H
ATOM 90 1HA GLY 1C 49.780 86.535 39.421 1.00 0.00
H
ATOM 91 2HA GLY 1C 51.414 87.090 39.842 1.00 0.00
H
ATOM 92 O GLY 2 50.081 89.233 37.785 1.00 0.00
O
ATOM 93 HO GLY 2 49.769 90.133 37.898 1.00 0.00
H
TER
ATOM 94 N GLY 1 11.093 76.967 23.302 1.00 0.00
N
ATOM 95 CA GLY 1 10.300 78.066 22.761 1.00 0.00
C
ATOM 96 C GLY 1 10.791 79.396 23.282 1.00 0.00
C
ATOM 97 O GLY 1 11.708 79.478 24.094 1.00 0.00
O
ATOM 98 1H GLY 1 11.821 77.343 23.928 1.00 0.00
H
ATOM 99 2H GLY 1 10.482 76.330 23.833 1.00 0.00
H
ATOM 100 1HA GLY 1 10.351 78.068 21.657 1.00 0.00
H
ATOM 101 2HA GLY 1 9.236 77.941 23.032 1.00 0.00
H
ATOM 102 N PRO 1B 10.176 80.462 22.814 1.00 0.00
N
ATOM 103 CA PRO 1B 10.540 81.812 23.212 1.00 0.00
C
ATOM 104 C PRO 1B 10.054 82.136 24.634 1.00 0.00
C
ATOM 105 O PRO 1B 9.005 81.651 25.061 1.00 0.00
O
ATOM 106 CB PRO 1B 9.775 82.661 22.185 1.00 0.00
C
ATOM 107 CG PRO 1B 8.544 81.804 21.851 1.00 0.00
C
ATOM 108 CD PRO 1B 9.097 80.378 21.852 1.00 0.00
C
ATOM 109 HA PRO 1B 11.623 81.944 23.173 1.00 0.00
H
ATOM 110 1HB PRO 1B 9.512 83.652 22.564 1.00 0.00
H
ATOM 111 2HB PRO 1B 10.390 82.773 21.288 1.00 0.00
H
ATOM 112 1HG PRO 1B 7.801 81.907 22.645 1.00 0.00
H
ATOM 113 2HG PRO 1B 8.095 82.073 20.892 1.00 0.00
H
ATOM 114 1HD PRO 1B 8.350 79.645 22.163 1.00 0.00
H
ATOM 115 2HD PRO 1B 9.502 80.114 20.872 1.00 0.00
H
ATOM 116 N GLY 1C 10.764 82.928 25.408 1.00 0.00
N
ATOM 117 CA GLY 1C 10.276 83.382 26.708 1.00 0.00
C
ATOM 118 C GLY 1C 9.807 84.816 26.639 1.00 0.00
C
ATOM 119 O GLY 1C 9.483 85.446 27.644 1.00 0.00
O
ATOM 120 H GLY 1C 11.693 83.239 25.089 1.00 0.00
H
ATOM 121 1HA GLY 1C 9.441 82.743 27.046 1.00 0.00
H
ATOM 122 2HA GLY 1C 11.074 83.297 27.467 1.00 0.00
H
ATOM 123 O GLY 2 9.742 85.440 25.410 1.00 0.00
O
ATOM 124 HO GLY 2 9.429 86.341 25.523 1.00 0.00
H
END
I also tryied to find out GLY16 residue but i didnt find anywhere in pdb
file.
Thanks!
Alok
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