[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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