[gmx-users] Capping (neuralising) of peptide

Alok alokjain at iitk.ac.in
Thu Sep 30 19:28:28 CEST 2004


Hello
     sorry to bother you again, sir!
I think there is some confusion regarding the simulation that I am doing.
So, I am describing again and it is as follows:
           I am trying to simulate four triplet peptides (Gly1-Pro-Gly2).
I have generated all the four peptides using InsightII and all
the four have different x,y and z coordinates.Also , I have
done the clipping of each peptides (i.e. NH2 in Gly1 and COOH
in Gly2).  Then I have generated  a pdb file in which all these
peptides are very far away from each other(in the sense of
coordinates).
when i used pdb2gmx -ignh  -f peptide.pdb -o peptide.gro  -p peptide.top
it genrates .gro and .top file but it also creates the bond between all
four peptides (which i dont want)
So, is there any option in gromacs to keep all these peptides seperately
as different seqments without creating peptide bond between them. (like
the "segment" flag in CHARMM)
I also checked it with pdb2gmx -ignh  -ter -f peptide.pdb -o peptide.gro
-p peptide.top but there too, the problem is same.

If I am not wrong then Dr. Peter Tieleman did the same with four
Alamethicin Helices using gromacs.

Kindly suggest me as to what is the alternative and how to proceed further.

Regards,
Alok



output of the pdb2gmx program is as follows:



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 12 residues with 64 atoms

  chain  #res #atoms
  1 ' '    12     64

All occupancies are one
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 peptidetest.top to ./#peptidetest.top.6#
Processing chain 1 (64 atoms, 12 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 20 hydrogen bonds
Checking for duplicate atoms....
deleting duplicate atom    O  GLY   3  pdb nr   30
deleting duplicate atom    O  GLY   6  pdb nr   61
deleting duplicate atom    O  GLY   9  pdb nr   92
deleting duplicate atom    O  GLY  12  pdb nr  123
Now there are 60 atoms
N-terminus: GLY-NH3+
C-terminus: COO-
Now there are 12 residues with 71 atoms
Making bonds...
Warning: Long Bond (18-20 = 4.40022 nm)
Warning: Long Bond (35-37 = 4.04127 nm)
Warning: Long Bond (52-54 = 4.36763 nm)
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Number of bonds was 79, now 74
Generating angles, dihedrals and pairs...
Before cleaning: 113 pairs
Before cleaning: 133 dihedrals
There are   51 dihedrals,   27 impropers,  107 angles
           113 pairs,       74 bonds and     0 dummies
Total mass 862.901 a.m.u.
Total charge 0.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.5#

Writing coordinate file...

Back Off! I just backed up peptide.gro to ./#peptide.gro.4#
                --------- PLEASE NOTE ------------
You have succesfully generated a topology from: peptide.pdb.
The select force field and the spc water model are used.
Note that the default mechanism for selecting a force fields has
changed, starting from GROMACS version 3.2.0
                --------- ETON ESAELP ------------

gcq#247: "Uh-oh" (Tinky Winky)




my PDB file :-


REMARK   4
REMARK   4 FINA COMPLIES WITH FORMAT V. 2.0, 30-SEP-2004
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     1C     13.704  35.373  29.853  1.00  0.00
  O
ATOM     31  HO  GLY     1C     13.391  36.273  29.966  1.00  0.00
  H
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
ATOM     61  O   GLY     1C     55.849  42.100  42.635  1.00  0.00
  O
ATOM     62  HO  GLY     1C     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     1C     50.081  89.233  37.785  1.00  0.00
  O
ATOM     93  HO  GLY     1C     49.769  90.133  37.898  1.00  0.00
  H
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     1C      9.742  85.440  25.410  1.00  0.00
  O
ATOM    124  HO  GLY     1C      9.429  86.341  25.523  1.00  0.00
  H
END








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