Problem to martinize a gemini peptide (302 atoms) #728

sergio-garay · 2025-08-31T15:16:41Z

sergio-garay
Aug 31, 2025

Hey there.

I've been working with a 302-atom Gemini peptide compound in GROMACS, using the AMBER99-IDLN force field. I'm trying to get a coarse-grained (CG) model for MARTINI3, but I'm having some trouble.

I'm giving Martinize2 two directories: force-fields and mappings. In the force-fields directory, I have a martini3 folder with an AG2.ff file and a charmm folder (even though the original is AMBER) with an AG2.ff file. In the mappings folder, I put the ag2.charmm36.map file.

Martinize2 starts the process but gets stuck in an internal loop ("correcting the graph") and never finishes.
This is the text I see on my screen:

> martinize2 -ff-dir force_fields -map-dir mappings -f AG2cis.pdb -x AG2-CG -o topol.top -v 
    INFO - general - vermouth.pdb.pdb - Read 1 molecules from PDB file AG2cis.pdb
    INFO - step - vermouth - Guessing the bonds.
    INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
   DEBUG - step - vermouth - Annotating required mutations and modifications.
 WARNING - general - vermouth.processors.annotate_mut_mod - Residue specified by "cter" for mutation "C-ter" not found
    INFO - step - vermouth - Repairing the graph.
   DEBUG - step - vermouth.processors.repair_graph - Making reference graph
   DEBUG - step - vermouth.processors.repair_graph - Matching residue A-AG21 to its reference

Any ideas on what I should do? Thanks for any help you can give me.

pckroon · 2025-09-01T08:52:25Z

pckroon
Sep 1, 2025
Maintainer

Could you run with -vv and get back? That may reveal a little more.
My initial guess is that the coordinates of residue A-AG21 are suspect. You can inspect it in (for example) vmd, be on the lookout for triangles.
Alternatively there's a problematic mismatch in atom naming between amber and charmm.

7 replies

sergio-garay Sep 1, 2025
Author

No, I do have some aminoacids inside my molecule, but they are not defined as that. I paste my pdb (302 atoms, taken from all atom MD, and edited of course), and my block definitions. I can't find a residue named AG21, because I didn't defined any residue. This is my very first time using Martini, and there are many things that I can't completely understand. Thank you for your time

PDB:

CRYST1   52.750   60.820   52.730  90.00  90.00  90.00 P 1           1
ATOM      1 C21a AG2 A   1      37.996  12.166  34.613  0.00  0.00           C
ATOM      2 O22a AG2 A   1      37.527  12.994  33.843  0.00  0.00           O
ATOM      3 C22a AG2 A   1      39.100  11.197  34.199  0.00  0.00           C
ATOM      4  H2a AG2 A   1      39.885  11.185  34.992  0.00  0.00           H
ATOM      5  H3a AG2 A   1      39.558  11.565  33.257  0.00  0.00           H
ATOM      6 C23a AG2 A   1      38.542   9.764  34.000  0.00  0.00           C
ATOM      7  H4a AG2 A   1      39.394   9.093  33.745  0.00  0.00           H
ATOM      8  H5a AG2 A   1      38.104   9.401  34.949  0.00  0.00           H
ATOM      9 C24a AG2 A   1      37.486   9.649  32.881  0.00  0.00           C
ATOM     10  H6a AG2 A   1      37.927   9.985  31.918  0.00  0.00           H
ATOM     11  H7a AG2 A   1      36.642  10.322  33.124  0.00  0.00           H
ATOM     12 C25a AG2 A   1      36.958   8.216  32.738  0.00  0.00           C
ATOM     13  H8a AG2 A   1      36.608   7.855  33.732  0.00  0.00           H
ATOM     14  H9a AG2 A   1      37.794   7.554  32.421  0.00  0.00           H
ATOM     15 C26a AG2 A   1      35.794   8.051  31.733  0.00  0.00           C
ATOM     16 H10a AG2 A   1      35.528   6.970  31.705  0.00  0.00           H
ATOM     17 H11a AG2 A   1      36.144   8.338  30.723  0.00  0.00           H
ATOM     18 C27a AG2 A   1      34.536   8.846  32.115  0.00  0.00           C
ATOM     19 H12a AG2 A   1      34.746   9.937  32.053  0.00  0.00           H
ATOM     20 H13a AG2 A   1      34.284   8.612  33.180  0.00  0.00           H
ATOM     21 C28a AG2 A   1      33.298   8.529  31.254  0.00  0.00           C
ATOM     22 H14a AG2 A   1      32.431   9.063  31.697  0.00  0.00           H
ATOM     23 H15a AG2 A   1      33.078   7.440  31.344  0.00  0.00           H
ATOM     24 C29a AG2 A   1      33.462   8.914  29.815  0.00  0.00           C
ATOM     25 H16a AG2 A   1      34.165   8.307  29.213  0.00  0.00           H
ATOM     26 C30a AG2 A   1      32.723   9.859  29.224  0.00  0.00           C
ATOM     27 H17a AG2 A   1      32.932  10.140  28.181  0.00  0.00           H
ATOM     28 C31a AG2 A   1      31.649  10.645  29.922  0.00  0.00           C
ATOM     29 H18a AG2 A   1      31.573  10.345  30.986  0.00  0.00           H
ATOM     30 H19a AG2 A   1      30.671  10.450  29.447  0.00  0.00           H
ATOM     31 C32a AG2 A   1      31.926  12.166  29.856  0.00  0.00           C
ATOM     32 H20a AG2 A   1      31.073  12.678  30.361  0.00  0.00           H
ATOM     33 H21a AG2 A   1      31.932  12.484  28.796  0.00  0.00           H
ATOM     34 C33a AG2 A   1      33.223  12.595  30.541  0.00  0.00           C
ATOM     35 H22a AG2 A   1      34.078  12.108  30.013  0.00  0.00           H
ATOM     36 H23a AG2 A   1      33.219  12.233  31.594  0.00  0.00           H
ATOM     37 C34a AG2 A   1      33.448  14.122  30.532  0.00  0.00           C
ATOM     38 H24a AG2 A   1      33.462  14.480  29.481  0.00  0.00           H
ATOM     39 H25a AG2 A   1      34.455  14.332  30.953  0.00  0.00           H
ATOM     40 C35a AG2 A   1      32.393  14.906  31.333  0.00  0.00           C
ATOM     41 H26a AG2 A   1      32.223  14.391  32.307  0.00  0.00           H
ATOM     42 H27a AG2 A   1      31.431  14.890  30.783  0.00  0.00           H
ATOM     43 C36a AG2 A   1      32.779  16.362  31.626  0.00  0.00           C
ATOM     44 H28a AG2 A   1      33.715  16.373  32.236  0.00  0.00           H
ATOM     45 H29a AG2 A   1      31.975  16.819  32.242  0.00  0.00           H
ATOM     46 C37a AG2 A   1      33.001  17.230  30.372  0.00  0.00           C
ATOM     47 H30a AG2 A   1      33.837  16.799  29.775  0.00  0.00           H
ATOM     48 H31a AG2 A   1      32.094  17.187  29.731  0.00  0.00           H
ATOM     49 C38a AG2 A   1      33.337  18.676  30.705  0.00  0.00           C
ATOM     50 H32a AG2 A   1      34.269  18.727  31.308  0.00  0.00           H
ATOM     51 H33a AG2 A   1      32.530  19.173  31.291  0.00  0.00           H
ATOM     52 H34a AG2 A   1      33.498  19.270  29.773  0.00  0.00           H
ATOM     53   Nb AG2 A   1      37.510  11.983  35.849  0.00  0.00           N
ATOM     54   Hb AG2 A   1      37.959  11.294  36.432  0.00  0.00           H
ATOM     55  CAb AG2 A   1      36.429  12.752  36.473  0.00  0.00           C
ATOM     56  HAb AG2 A   1      36.410  13.753  36.054  0.00  0.00           H
ATOM     57  CBb AG2 A   1      35.076  12.078  36.184  0.00  0.00           C
ATOM     58 HB1b AG2 A   1      34.939  12.004  35.101  0.00  0.00           H
ATOM     59 HB2b AG2 A   1      35.089  11.066  36.581  0.00  0.00           H
ATOM     60  CGb AG2 A   1      33.884  12.791  36.753  0.00  0.00           C
ATOM     61 CD1b AG2 A   1      33.126  13.699  36.096  0.00  0.00           C
ATOM     62 HD1b AG2 A   1      33.271  13.991  35.056  0.00  0.00           H
ATOM     63 NE1b AG2 A   1      32.145  14.180  36.931  0.00  0.00           N
ATOM     64 HE1b AG2 A   1      31.452  14.878  36.644  0.00  0.00           H
ATOM     65 CE2b AG2 A   1      32.212  13.616  38.187  0.00  0.00           C
ATOM     66 CZ2b AG2 A   1      31.471  13.785  39.353  0.00  0.00           C
ATOM     67 HZ2b AG2 A   1      30.647  14.493  39.380  0.00  0.00           H
ATOM     68 CH2b AG2 A   1      31.806  13.041  40.494  0.00  0.00           C
ATOM     69 HH2b AG2 A   1      31.242  13.176  41.410  0.00  0.00           H
ATOM     70 CZ3b AG2 A   1      32.869  12.129  40.442  0.00  0.00           C
ATOM     71 HZ3b AG2 A   1      33.123  11.552  41.326  0.00  0.00           H
ATOM     72 CE3b AG2 A   1      33.618  11.962  39.264  0.00  0.00           C
ATOM     73 HE3b AG2 A   1      34.435  11.266  39.234  0.00  0.00           H
ATOM     74 CD2b AG2 A   1      33.308  12.707  38.096  0.00  0.00           C
ATOM     75   Cb AG2 A   1      36.671  12.857  37.982  0.00  0.00           C
ATOM     76   Ob AG2 A   1      37.145  11.895  38.593  0.00  0.00           O
ATOM     77   Nc AG2 A   1      36.327  13.999  38.586  0.00  0.00           N
ATOM     78   Hc AG2 A   1      35.844  14.695  38.051  0.00  0.00           H
ATOM     79  CAc AG2 A   1      36.556  14.291  40.011  0.00  0.00           C
ATOM     80  HAc AG2 A   1      36.534  13.352  40.574  0.00  0.00           H
ATOM     81  CBc AG2 A   1      37.933  14.959  40.210  0.00  0.00           C
ATOM     82 HB1c AG2 A   1      38.112  15.049  41.282  0.00  0.00           H
ATOM     83 HB2c AG2 A   1      37.885  15.968  39.797  0.00  0.00           H
ATOM     84  CGc AG2 A   1      39.108  14.263  39.589  0.00  0.00           C
ATOM     85 CD1c AG2 A   1      39.939  13.391  40.200  0.00  0.00           C
ATOM     86 HD1c AG2 A   1      39.846  13.064  41.235  0.00  0.00           H
ATOM     87 NE1c AG2 A   1      40.875  12.924  39.293  0.00  0.00           N
ATOM     88 HE1c AG2 A   1      41.556  12.200  39.512  0.00  0.00           H
ATOM     89 CE2c AG2 A   1      40.694  13.476  38.051  0.00  0.00           C
ATOM     90 CZ2c AG2 A   1      41.349  13.303  36.821  0.00  0.00           C
ATOM     91 HZ2c AG2 A   1      42.191  12.628  36.743  0.00  0.00           H
ATOM     92 CH2c AG2 A   1      40.894  14.016  35.702  0.00  0.00           C
ATOM     93 HH2c AG2 A   1      41.383  13.890  34.752  0.00  0.00           H
ATOM     94 CZ3c AG2 A   1      39.792  14.884  35.822  0.00  0.00           C
ATOM     95 HZ3c AG2 A   1      39.432  15.421  34.952  0.00  0.00           H
ATOM     96 CE3c AG2 A   1      39.157  15.064  37.058  0.00  0.00           C
ATOM     97 HE3c AG2 A   1      38.309  15.726  37.138  0.00  0.00           H
ATOM     98 CD2c AG2 A   1      39.580  14.355  38.208  0.00  0.00           C
ATOM     99   Cc AG2 A   1      35.464  15.216  40.564  0.00  0.00           C
ATOM    100   Oc AG2 A   1      34.957  16.078  39.855  0.00  0.00           O
ATOM    101   Nd AG2 A   1      35.185  15.112  41.869  0.00  0.00           N
ATOM    102   Hd AG2 A   1      35.651  14.375  42.391  0.00  0.00           H
ATOM    103  CAd AG2 A   1      34.242  15.962  42.618  0.00  0.00           C
ATOM    104  HAd AG2 A   1      33.339  16.081  42.011  0.00  0.00           H
ATOM    105  CBd AG2 A   1      33.843  15.216  43.907  0.00  0.00           C
ATOM    106 HB1d AG2 A   1      33.046  15.777  44.406  0.00  0.00           H
ATOM    107 HB2d AG2 A   1      34.703  15.207  44.578  0.00  0.00           H
ATOM    108  SGd AG2 A   1      33.294  13.503  43.671  0.00  0.00           S
ATOM    109   Cd AG2 A   1      34.818  17.376  42.869  0.00  0.00           C
ATOM    110   Od AG2 A   1      34.971  17.816  44.017  0.00  0.00           O
ATOM    111   Nf AG2 A   1      35.243  18.073  41.799  0.00  0.00           N
ATOM    112   Hf AG2 A   1      35.059  17.640  40.895  0.00  0.00           H
ATOM    113  CAf AG2 A   1      36.142  19.243  41.848  0.00  0.00           C
ATOM    114  HAf AG2 A   1      36.914  18.992  42.588  0.00  0.00           H
ATOM    115  CBf AG2 A   1      36.869  19.417  40.499  0.00  0.00           C
ATOM    116 HB1f AG2 A   1      37.330  18.470  40.215  0.00  0.00           H
ATOM    117 HB2f AG2 A   1      37.677  20.142  40.642  0.00  0.00           H
ATOM    118  CGf AG2 A   1      35.986  19.912  39.336  0.00  0.00           C
ATOM    119 HG1f AG2 A   1      35.560  20.884  39.589  0.00  0.00           H
ATOM    120 HG2f AG2 A   1      35.171  19.202  39.166  0.00  0.00           H
ATOM    121  CDf AG2 A   1      36.799  20.073  38.046  0.00  0.00           C
ATOM    122 HD1f AG2 A   1      37.696  20.659  38.266  0.00  0.00           H
ATOM    123 HD2f AG2 A   1      37.120  19.086  37.706  0.00  0.00           H
ATOM    124  NEf AG2 A   1      36.015  20.743  36.974  0.00  0.00           N
ATOM    125 HE1f AG2 A   1      35.770  21.689  37.236  0.00  0.00           H
ATOM    126 HE2f AG2 A   1      35.162  20.231  36.758  0.00  0.00           H
ATOM    127 HE3f AG2 A   1      36.538  20.808  36.100  0.00  0.00           H
ATOM    128   Cf AG2 A   1      35.478  20.533  42.336  0.00  0.00           C
ATOM    129   Of AG2 A   1      34.376  20.863  41.916  0.00  0.00           O
ATOM    130   Ng AG2 A   1      36.224  21.294  43.157  0.00  0.00           N
ATOM    131   Hg AG2 A   1      37.054  20.847  43.525  0.00  0.00           H
ATOM    132  CAg AG2 A   1      35.885  22.613  43.723  0.00  0.00           C
ATOM    133  HAg AG2 A   1      35.161  22.464  44.525  0.00  0.00           H
ATOM    134  CBg AG2 A   1      37.176  23.221  44.325  0.00  0.00           C
ATOM    135 HB1g AG2 A   1      37.923  23.328  43.540  0.00  0.00           H
ATOM    136 HB2g AG2 A   1      37.567  22.519  45.075  0.00  0.00           H
ATOM    137  CGg AG2 A   1      36.964  24.587  45.010  0.00  0.00           C
ATOM    138 HG1g AG2 A   1      36.152  24.490  45.734  0.00  0.00           H
ATOM    139 HG2g AG2 A   1      36.683  25.338  44.270  0.00  0.00           H
ATOM    140  CDg AG2 A   1      38.222  25.049  45.777  0.00  0.00           C
ATOM    141 HD1g AG2 A   1      37.940  25.901  46.405  0.00  0.00           H
ATOM    142 HD2g AG2 A   1      38.536  24.247  46.441  0.00  0.00           H
ATOM    143  NEg AG2 A   1      39.336  25.445  44.891  0.00  0.00           N
ATOM    144 HE1g AG2 A   1      39.636  24.691  44.288  0.00  0.00           H
ATOM    145 HE2g AG2 A   1      39.082  26.214  44.281  0.00  0.00           H
ATOM    146 HE3g AG2 A   1      40.144  25.726  45.439  0.00  0.00           H
ATOM    147   Cg AG2 A   1      35.257  23.534  42.677  0.00  0.00           C
ATOM    148   Og AG2 A   1      35.854  23.796  41.634  0.00  0.00           O
ATOM    149   Nh AG2 A   1      34.071  24.058  42.962  0.00  0.00           N
ATOM    150  H1h AG2 A   1      33.613  24.628  42.276  0.00  0.00           H
ATOM    151  H2h AG2 A   1      33.591  23.758  43.789  0.00  0.00           H
ATOM    152 C21i AG2 A   1      32.732   8.336  44.662  0.00  0.00           C
ATOM    153 O22i AG2 A   1      31.977   9.187  45.096  0.00  0.00           O
ATOM    154 C22i AG2 A   1      33.847   8.660  43.667  0.00  0.00           C
ATOM    155  H2i AG2 A   1      34.710   7.971  43.812  0.00  0.00           H
ATOM    156  H3i AG2 A   1      34.188   9.691  43.913  0.00  0.00           H
ATOM    157 C23i AG2 A   1      33.323   8.626  42.220  0.00  0.00           C
ATOM    158  H4i AG2 A   1      32.334   9.130  42.183  0.00  0.00           H
ATOM    159  H5i AG2 A   1      34.019   9.223  41.576  0.00  0.00           H
ATOM    160 C24i AG2 A   1      33.210   7.228  41.605  0.00  0.00           C
ATOM    161  H6i AG2 A   1      32.658   7.323  40.633  0.00  0.00           H
ATOM    162  H7i AG2 A   1      32.579   6.576  42.266  0.00  0.00           H
ATOM    163 C25i AG2 A   1      34.555   6.545  41.336  0.00  0.00           C
ATOM    164  H8i AG2 A   1      35.137   6.463  42.279  0.00  0.00           H
ATOM    165  H9i AG2 A   1      35.147   7.188  40.637  0.00  0.00           H
ATOM    166 C26i AG2 A   1      34.405   5.135  40.737  0.00  0.00           C
ATOM    167 H10i AG2 A   1      33.757   5.183  39.829  0.00  0.00           H
ATOM    168 H11i AG2 A   1      33.888   4.493  41.480  0.00  0.00           H
ATOM    169 C27i AG2 A   1      35.746   4.488  40.350  0.00  0.00           C
ATOM    170 H12i AG2 A   1      36.447   4.551  41.214  0.00  0.00           H
ATOM    171 H13i AG2 A   1      36.207   5.051  39.514  0.00  0.00           H
ATOM    172 C28i AG2 A   1      35.589   3.018  39.944  0.00  0.00           C
ATOM    173 H14i AG2 A   1      34.926   2.962  39.046  0.00  0.00           H
ATOM    174 H15i AG2 A   1      35.078   2.469  40.764  0.00  0.00           H
ATOM    175 C29i AG2 A   1      36.918   2.382  39.664  0.00  0.00           C
ATOM    176 H16i AG2 A   1      37.657   2.380  40.480  0.00  0.00           H
ATOM    177 C30i AG2 A   1      37.240   1.839  38.471  0.00  0.00           C
ATOM    178 H17i AG2 A   1      38.229   1.378  38.333  0.00  0.00           H
ATOM    179 C31i AG2 A   1      36.318   1.803  37.285  0.00  0.00           C
ATOM    180 H18i AG2 A   1      36.798   2.302  36.420  0.00  0.00           H
ATOM    181 H19i AG2 A   1      35.362   2.335  37.484  0.00  0.00           H
ATOM    182 C32i AG2 A   1      35.992   0.358  36.869  0.00  0.00           C
ATOM    183 H20i AG2 A   1      36.943  -0.220  36.738  0.00  0.00           H
ATOM    184 H21i AG2 A   1      35.479   0.388  35.876  0.00  0.00           H
ATOM    185 C33i AG2 A   1      35.077  -0.375  37.865  0.00  0.00           C
ATOM    186 H22i AG2 A   1      34.149   0.229  38.004  0.00  0.00           H
ATOM    187 H23i AG2 A   1      35.597  -0.455  38.840  0.00  0.00           H
ATOM    188 C34i AG2 A   1      34.684  -1.775  37.374  0.00  0.00           C
ATOM    189 H24i AG2 A   1      35.629  -2.349  37.189  0.00  0.00           H
ATOM    190 H25i AG2 A   1      34.155  -1.697  36.404  0.00  0.00           H
ATOM    191 C35i AG2 A   1      33.819  -2.571  38.366  0.00  0.00           C
ATOM    192 H26i AG2 A   1      34.329  -2.611  39.352  0.00  0.00           H
ATOM    193 H27i AG2 A   1      33.745  -3.615  37.984  0.00  0.00           H
ATOM    194 C36i AG2 A   1      32.401  -2.017  38.530  0.00  0.00           C
ATOM    195 H28i AG2 A   1      31.930  -1.911  37.526  0.00  0.00           H
ATOM    196 H29i AG2 A   1      32.443  -1.002  38.977  0.00  0.00           H
ATOM    197 C37i AG2 A   1      31.507  -2.919  39.398  0.00  0.00           C
ATOM    198 H30i AG2 A   1      31.336  -3.874  38.845  0.00  0.00           H
ATOM    199 H31i AG2 A   1      32.051  -3.172  40.334  0.00  0.00           H
ATOM    200 C38i AG2 A   1      30.167  -2.303  39.771  0.00  0.00           C
ATOM    201 H32i AG2 A   1      29.557  -3.022  40.354  0.00  0.00           H
ATOM    202 H33i AG2 A   1      29.595  -2.022  38.854  0.00  0.00           H
ATOM    203 H34i AG2 A   1      30.315  -1.397  40.399  0.00  0.00           H
ATOM    204   Nj AG2 A   1      32.699   7.087  45.133  0.00  0.00           N
ATOM    205   Hj AG2 A   1      33.369   6.417  44.775  0.00  0.00           H
ATOM    206  CAj AG2 A   1      31.694   6.590  46.089  0.00  0.00           C
ATOM    207  HAj AG2 A   1      30.707   6.808  45.673  0.00  0.00           H
ATOM    208  CBj AG2 A   1      31.821   5.068  46.227  0.00  0.00           C
ATOM    209 HB1j AG2 A   1      31.030   4.703  46.870  0.00  0.00           H
ATOM    210 HB2j AG2 A   1      31.667   4.618  45.251  0.00  0.00           H
ATOM    211  CGj AG2 A   1      33.130   4.567  46.765  0.00  0.00           C
ATOM    212 CD1j AG2 A   1      33.430   4.370  48.063  0.00  0.00           C
ATOM    213 HD1j AG2 A   1      32.745   4.532  48.890  0.00  0.00           H
ATOM    214 NE1j AG2 A   1      34.709   3.873  48.185  0.00  0.00           N
ATOM    215 HE1j AG2 A   1      35.109   3.562  49.053  0.00  0.00           H
ATOM    216 CE2j AG2 A   1      35.313   3.732  46.944  0.00  0.00           C
ATOM    217 CZ2j AG2 A   1      36.577   3.281  46.536  0.00  0.00           C
ATOM    218 HZ2j AG2 A   1      37.310   2.968  47.271  0.00  0.00           H
ATOM    219 CH2j AG2 A   1      36.872   3.225  45.174  0.00  0.00           C
ATOM    220 HH2j AG2 A   1      37.843   2.883  44.838  0.00  0.00           H
ATOM    221 CZ3j AG2 A   1      35.899   3.591  44.219  0.00  0.00           C
ATOM    222 HZ3j AG2 A   1      36.123   3.515  43.172  0.00  0.00           H
ATOM    223 CE3j AG2 A   1      34.634   4.052  44.637  0.00  0.00           C
ATOM    224 HE3j AG2 A   1      33.890   4.305  43.899  0.00  0.00           H
ATOM    225 CD2j AG2 A   1      34.313   4.146  46.007  0.00  0.00           C
ATOM    226   Cj AG2 A   1      31.735   7.260  47.472  0.00  0.00           C
ATOM    227   Oj AG2 A   1      30.820   7.082  48.281  0.00  0.00           O
ATOM    228   Nk AG2 A   1      32.781   8.036  47.769  0.00  0.00           N
ATOM    229   Hk AG2 A   1      33.494   8.127  47.053  0.00  0.00           H
ATOM    230  CAk AG2 A   1      32.907   8.877  48.959  0.00  0.00           C
ATOM    231  HAk AG2 A   1      32.390   8.396  49.790  0.00  0.00           H
ATOM    232  CBk AG2 A   1      34.394   8.975  49.332  0.00  0.00           C
ATOM    233 HB1k AG2 A   1      34.765   7.980  49.573  0.00  0.00           H
ATOM    234 HB2k AG2 A   1      34.488   9.583  50.236  0.00  0.00           H
ATOM    235  CGk AG2 A   1      35.297   9.560  48.278  0.00  0.00           C
ATOM    236 CD1k AG2 A   1      35.693  10.843  48.214  0.00  0.00           C
ATOM    237 HD1k AG2 A   1      35.422  11.618  48.922  0.00  0.00           H
ATOM    238 NE1k AG2 A   1      36.555  11.015  47.146  0.00  0.00           N
ATOM    239 HE1k AG2 A   1      37.071  11.874  46.977  0.00  0.00           H
ATOM    240 CE2k AG2 A   1      36.712   9.850  46.429  0.00  0.00           C
ATOM    241 CZ2k AG2 A   1      37.443   9.520  45.273  0.00  0.00           C
ATOM    242 HZ2k AG2 A   1      38.028  10.270  44.778  0.00  0.00           H
ATOM    243 CH2k AG2 A   1      37.424   8.187  44.810  0.00  0.00           C
ATOM    244 HH2k AG2 A   1      37.987   7.922  43.935  0.00  0.00           H
ATOM    245 CZ3k AG2 A   1      36.679   7.215  45.504  0.00  0.00           C
ATOM    246 HZ3k AG2 A   1      36.697   6.198  45.153  0.00  0.00           H
ATOM    247 CE3k AG2 A   1      35.940   7.557  46.659  0.00  0.00           C
ATOM    248 HE3k AG2 A   1      35.397   6.788  47.179  0.00  0.00           H
ATOM    249 CD2k AG2 A   1      35.930   8.883  47.143  0.00  0.00           C
ATOM    250   Ck AG2 A   1      32.271  10.271  48.794  0.00  0.00           C
ATOM    251   Ok AG2 A   1      32.023  10.951  49.788  0.00  0.00           O
ATOM    252   Nl AG2 A   1      31.963  10.704  47.559  0.00  0.00           N
ATOM    253   Hl AG2 A   1      32.130  10.098  46.761  0.00  0.00           H
ATOM    254  CAl AG2 A   1      31.196  11.926  47.334  0.00  0.00           C
ATOM    255  HAl AG2 A   1      31.577  12.693  48.011  0.00  0.00           H
ATOM    256  CBl AG2 A   1      31.456  12.446  45.905  0.00  0.00           C
ATOM    257 HB1l AG2 A   1      30.929  13.389  45.764  0.00  0.00           H
ATOM    258 HB2l AG2 A   1      31.061  11.712  45.191  0.00  0.00           H
ATOM    259  SGl AG2 A   1      33.226  12.695  45.552  0.00  0.00           S
ATOM    260   Cl AG2 A   1      29.719  11.694  47.670  0.00  0.00           C
ATOM    261   Ol AG2 A   1      29.190  10.587  47.510  0.00  0.00           O
ATOM    262   Nm AG2 A   1      29.048  12.716  48.219  0.00  0.00           N
ATOM    263   Hm AG2 A   1      29.577  13.579  48.334  0.00  0.00           H
ATOM    264  CAm AG2 A   1      27.789  12.606  49.000  0.00  0.00           C
ATOM    265  HAm AG2 A   1      27.573  13.612  49.349  0.00  0.00           H
ATOM    266  CBm AG2 A   1      26.579  12.178  48.144  0.00  0.00           C
ATOM    267 HB1m AG2 A   1      25.690  12.196  48.767  0.00  0.00           H
ATOM    268 HB2m AG2 A   1      26.719  11.155  47.791  0.00  0.00           H
ATOM    269  CGm AG2 A   1      26.310  13.091  46.945  0.00  0.00           C
ATOM    270 HG1m AG2 A   1      27.140  13.022  46.242  0.00  0.00           H
ATOM    271 HG2m AG2 A   1      26.179  14.125  47.280  0.00  0.00           H
ATOM    272  CDm AG2 A   1      25.023  12.599  46.276  0.00  0.00           C
ATOM    273 HD1m AG2 A   1      25.097  11.514  46.126  0.00  0.00           H
ATOM    274 HD2m AG2 A   1      24.166  12.788  46.942  0.00  0.00           H
ATOM    275  NEm AG2 A   1      24.792  13.239  44.965  0.00  0.00           N
ATOM    276 HE1m AG2 A   1      25.585  13.057  44.360  0.00  0.00           H
ATOM    277 HE2m AG2 A   1      24.630  14.242  45.060  0.00  0.00           H
ATOM    278 HE3m AG2 A   1      23.985  12.795  44.523  0.00  0.00           H
ATOM    279   Cm AG2 A   1      27.900  11.776  50.290  0.00  0.00           C
ATOM    280   Om AG2 A   1      26.879  11.408  50.868  0.00  0.00           O
ATOM    281   Nn AG2 A   1      29.114  11.530  50.808  0.00  0.00           N
ATOM    282   Hn AG2 A   1      29.927  11.842  50.282  0.00  0.00           H
ATOM    283  CAn AG2 A   1      29.358  11.024  52.167  0.00  0.00           C
ATOM    284  HAn AG2 A   1      28.405  10.901  52.678  0.00  0.00           H
ATOM    285  CBn AG2 A   1      30.053   9.651  52.157  0.00  0.00           C
ATOM    286 HB1n AG2 A   1      30.059   9.264  53.179  0.00  0.00           H
ATOM    287 HB2n AG2 A   1      31.095   9.762  51.847  0.00  0.00           H
ATOM    288  CGn AG2 A   1      29.364   8.634  51.243  0.00  0.00           C
ATOM    289 HG1n AG2 A   1      29.509   8.925  50.203  0.00  0.00           H
ATOM    290 HG2n AG2 A   1      28.298   8.611  51.458  0.00  0.00           H
ATOM    291  CDn AG2 A   1      29.945   7.233  51.456  0.00  0.00           C
ATOM    292 HD1n AG2 A   1      31.033   7.264  51.319  0.00  0.00           H
ATOM    293 HD2n AG2 A   1      29.752   6.926  52.494  0.00  0.00           H
ATOM    294  NEn AG2 A   1      29.356   6.251  50.523  0.00  0.00           N
ATOM    295 HE1n AG2 A   1      28.343   6.248  50.604  0.00  0.00           H
ATOM    296 HE2n AG2 A   1      29.627   6.465  49.564  0.00  0.00           H
ATOM    297 HE3n AG2 A   1      29.678   5.299  50.719  0.00  0.00           H
ATOM    298   Cn AG2 A   1      30.140  12.076  52.980  0.00  0.00           C
ATOM    299   On AG2 A   1      30.734  12.990  52.420  0.00  0.00           O
ATOM    300   No AG2 A   1      30.112  11.952  54.298  0.00  0.00           N
ATOM    301  H1o AG2 A   1      30.605  12.625  54.858  0.00  0.00           H
ATOM    302  H2o AG2 A   1      29.583  11.205  54.728  0.00  0.00           H
END

my block file

;;; AG2
[ moleculetype ]
AG2   1

[ atoms ]
; id type resnr residue atom cgnr charge
 1   SC1  1     AG2     SC1a    1   0
 2   SC1  1     AG2     SC1b    1   0
 3   C4h  1     AG2     C4ha    1   0
 4   C1   1     AG2     C1a     1   0
 5   C1   1     AG2     C1b     1   0
 6   P2   1     AG2     P2a     1   0
 7   TC4  1     AG2     TC4a    1   0
 8   TN6D 1     AG2     TN6da   1   0
 9   TC5  1     AG2     TC5a    1   0
 10  TC5  1     AG2     TC5b    1   0
 11  TC5  1     AG2     TC5c    1   0
 12  P2   1     AG2     P2b     1   0
 13  TC4  1     AG2     TC4b    1   0
 14  TN6d 1     AG2     TN6db   1   0
 15  TC5  1     AG2     TC5d    1   0
 16  TC5  1     AG2     TC5e    1   0
 17  TC5  1     AG2     TC5f    1   0
 18  P2   1     AG2     P2c     1   0
 19  TC6  1     AG2     TC6a    1   0
 20  P2   1     AG2     P2d     1   0
 21  SC2  1     AG2     SC2a    1   0
 22  SQ4p 1     AG2     SQ4pa   1   1
 23  P2   1     AG2     P2e     1   0
 24  SC2  1     AG2     SC2b    1   0
 25  SQ4p 1     AG2     SQ4pb   1   1
 26  P2   1     AG2     P2f     1   0
 27  SC1  1     AG2     SC1c    1   0
 28  SC1  1     AG2     SC1d    1   0
 29  C4h  1     AG2     C4hb    1   0
 30  C1   1     AG2     C1c     1   0
 31  C1   1     AG2     C1d     1   0
 32  P2   1     AG2     P2g     1   0
 33  TC4  1     AG2     TC4c    1   0
 34  TN6d 1     AG2     TN6dc   1   0
 35  TC5  1     AG2     TC5g    1   0
 36  TC5  1     AG2     TC5h    1   0
 37  TC5  1     AG2     TC5i    1   0
 38  P2   1     AG2     P2h     1   0
 39  TC4  1     AG2     TC4d    1   0
 40  TN6d 1     AG2     TN6dd   1   0
 41  TC5  1     AG2     TC5j    1   0
 42  TC5  1     AG2     TC5k    1   0
 43  TC5  1     AG2     TC5l    1   0
 44  P2   1     AG2     P2i     1   0
 45  TC6  1     AG2     TC6b    1   0
 46  P2   1     AG2     P2j     1   0
 47  SC2  1     AG2     SC2c    1   0
 48  SQ4p 1     AG2     SQ4pc   1   1
 49  P2   1     AG2     P2k     1   0
 50  SC2  1     AG2     SC2d    1   0
 51  SQ4p 1     AG2     SQ4pd   1   1
 52  P2   1     AG2     P2l     1   0
 
[ bonds ]
SC1a     SC1b     1     0.47    5000
SC1a     P2a      1     0.47    5000 ; REVISAR, NO ENCONTRÉ NADA PARECIDO
C1b      C4ha     1     0.47    3800    
C4ha     C1a      1     0.47    3800    
C1a      C1b      1     0.47    5000    
P2a      P2b      1     0.35    4000
P2a      TC4a     1     0.325   5000
TC4a     TN6da    1     0.32    1000000 ; STIFF
TC4a     TC5b     1     0.30    1000000 ; STIFF
TN6da    TC5b     1     0.27    1000000 ; STIFF
TN6da    TC5c     1     0.27    1000000 ; STIFF
TC5b     TC5c     1     0.293   1000000 ; STIFF
P2b      TC4b     1     0.325   5000
TC4b     TN6db    1     0.32    1000000 ; STIFF
TC4b     TC5e     1     0.30    1000000 ; STIFF
TN6db    TC5f     1     0.27    1000000 ; STIFF
TN6db    TC5e     1     0.27    1000000 ; STIFF
TC5e     TC5f     1     0.293   1000000 ; STIFF
P2b      P2c      1     0.35    4000
P2c      TC6a     1     0.341   7500 ; cys
P2c      P2d      1     0.35    4000
SC2a     SQ4pa    1     0.36    5000 ; tomado de lys, pero en lugar de SC3 el nuestro es SC2
P2d      P2e      1     0.35    4000
P2e      SC2b     1     0.341   7500
SC2b     SQ4pb    1     0.36    5000
P2e      P2f      1     0.35    4000
C1c      C1d      1     0.47    5000    
C1d      C4hb     1     0.47    3800    
C4hb     C1c      1     0.47    3800   
P2g      P2h      1     0.35    4000
P2g      TC4c     1     0.325   5000
TC4c     TN6dc    1     0.32    1000000 ; STIFF
TC4c     TC5h     1     0.30    1000000 ; STIFF
TN6db    TC5i     1     0.27    1000000 ; STIFF
TN6db    TC5h     1     0.27    1000000 ; STIFF
TC5h     TC5i     1     0.293   1000000 ; STIFF
P2g      P2h      1     0.35    4000
P2h      TC4d     1     0.325   5000
TC4d     TN6dd    1     0.32    1000000 ; STIFF
TC4c     TC5k     1     0.30    1000000 ; STIFF
TN6db    TC5l     1     0.27    1000000 ; STIFF
TN6db    TC5k     1     0.27    1000000 ; STIFF
TC5k     TC5l     1     0.293   1000000 ; STIFF
P2h      P2i      1     0.35    4000
P2i      TC6b     1     0.341   7500 ; cys
TC6b     TC6a     1     0.24    5000 ; CYS-BRIDGE constraint
P2i      P2j      1     0.35    4000
P2j      SC2c     1     0.341   1000000 (figura asi en ILE)
SC2c     SQ4pc    1     0.36    5000
P2j      P2k      1     0.35    4000
P2k      SC2d     1     0.341   1000000 (figura asi en ILE)
SC2d     SQ4pd    1     0.36    5000
P2k      P2l      1     0.35    4000

pckroon Sep 2, 2025
Maintainer

Right. So, in the image, which part is AG2? If it's the whole thing that'll be the reason martinize2 is suffering. Some of the steps we take scale very poorly with residue size.
What you could do instead is split your big residue (AG2) into separate aminoacid residues, and (optionally) using the regular amino acid blocks. However, you assign the full peptide bonds to single beads, so you'd get a slightly different model. That all said, what reason do you have to not use the regular amino acid parameters?
At the very least, splitting it into two residues across the disulfide bond will make things faster.

sergio-garay Sep 2, 2025
Author

Hey Peter,

The main reason I didn't separate my molecule into residues is that I thought it would be the easiest way to handle it, but it's clearly not.

I'm going to follow this tutorial: https://vermouth-martinize.readthedocs.io/en/latest/tutorials/6_adding_residues_links/index.html to introduce the modified residues: Ornithine (which I'll call ORN) and Oleic (OLE).

According to the tutorial, should I add one file with the modified residues (ORN, OLE), or should I have a separate file for each one?

Also, I see in the tutorial that only [ atoms ] and [ bonds ] are declared, and I don't see [ angles ] or [ dih ]. Is that correct?

Thanks for any help you can give me.

Sergio

pckroon Sep 2, 2025
Maintainer

Hi Sergio,
that sounds like a better plan ;)
You need to add the residues in 2 places, at the atomistic level, and at the cg level. The atomistic level doesn't need or use angles/dihedrals, just the atom names and bonds --- even the bond lengths and strengths don't matter. At the CG level bonded parameters are important.
It doesn't matter if you add ORN and OLE to the same file or separately. You will need separate files for the atomistic and cg levels though.

sergio-garay Sep 2, 2025
Author

Thank you very much Peter! I'll try.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Problem to martinize a gemini peptide (302 atoms) #728

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{editor}}'s edit

{{editor}}'s edit

Uh oh!

Replies: 1 comment 7 replies

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{editor}}'s edit

{{editor}}'s edit

Uh oh!

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{title}}

Uh oh!

Select a reply

Uh oh!

Problem to martinize a gemini peptide (302 atoms) #728

Uh oh!

Uh oh!

sergio-garay Aug 31, 2025

Replies: 1 comment · 7 replies

Uh oh!

pckroon Sep 1, 2025 Maintainer

Uh oh!

Uh oh!

sergio-garay Sep 1, 2025 Author

Uh oh!

pckroon Sep 2, 2025 Maintainer

Uh oh!

sergio-garay Sep 2, 2025 Author

Uh oh!

pckroon Sep 2, 2025 Maintainer

Uh oh!

sergio-garay Sep 2, 2025 Author

sergio-garay
Aug 31, 2025

Replies: 1 comment 7 replies

pckroon
Sep 1, 2025
Maintainer

sergio-garay Sep 1, 2025
Author

pckroon Sep 2, 2025
Maintainer

sergio-garay Sep 2, 2025
Author

pckroon Sep 2, 2025
Maintainer

sergio-garay Sep 2, 2025
Author