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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Final atom numbering in PQR is incorrect #132

Closed dvdesolve closed 3 years ago

dvdesolve commented 3 years ago

Seems like final numbering in PQR file is incorrect. This is what I get after running PDB2PQR (just a first 50 lines):

ATOM      1  N   SER     1      27.496  31.222  28.262  0.1849 1.8240
ATOM      2  CA  SER     1      27.785  31.042  26.803  0.0567 1.9080
ATOM      3  C   SER     1      27.906  29.537  26.564  0.6163 1.9080
ATOM      4  O   SER     1      27.364  28.975  25.640 -0.5722 1.6612
ATOM      5  CB  SER     1      29.012  31.766  26.331  0.2596 1.9080
ATOM      6  OG  SER     1      30.194  31.000  26.253 -0.6714 1.7210
ATOM      1  H1  SER     1      26.542  31.486  28.372  0.1898 0.6000
ATOM      1  HA  SER     1      27.004  31.377  26.304  0.0782 1.1000
ATOM      1  HB2 SER     1      28.830  32.161  25.408  0.0273 1.3870
ATOM      1  HB3 SER     1      29.189  32.557  26.951  0.0273 1.3870
ATOM      1  H2  SER     1      27.668  30.363  28.734  0.1898 0.6000
ATOM      1  H3  SER     1      28.090  31.934  28.624  0.1898 0.6000
ATOM      1  HG  SER     1      30.208  30.327  26.993  0.4239 0.0000
ATOM      7  N   SER     2      28.564  28.878  27.515 -0.4157 1.8240
ATOM      8  CA  SER     2      28.674  27.433  27.549 -0.0249 1.9080
ATOM      9  C   SER     2      27.273  26.844  27.733  0.5973 1.9080
ATOM     10  O   SER     2      26.826  25.801  27.202 -0.5679 1.6612
ATOM     11  CB  SER     2      29.652  27.146  28.701  0.2117 1.9080
ATOM     12  OG  SER     2      30.387  28.338  29.025 -0.6546 1.7210
ATOM      7  H   SER     2      28.998  29.502  28.241  0.2719 0.6000
ATOM      7  HA  SER     2      29.021  27.119  26.668  0.0843 1.3870
ATOM      7  HB2 SER     2      29.139  26.863  29.496  0.0352 1.3870
ATOM      7  HB3 SER     2      30.290  26.448  28.414  0.0352 1.3870
ATOM      7  HG  SER     2      30.021  28.725  29.866  0.4275 0.0000
ATOM     13  N   SER     3      26.416  27.561  28.467 -0.4157 1.8240
ATOM     14  CA  SER     3      25.057  27.186  28.762 -0.0249 1.9080
ATOM     15  C   SER     3      24.015  27.530  27.716  0.5973 1.9080
ATOM     16  O   SER     3      22.865  27.149  27.837 -0.5679 1.6612
ATOM     17  CB  SER     3      24.630  27.947  30.050  0.2117 1.9080
ATOM     18  OG  SER     3      25.560  27.616  31.064 -0.6546 1.7210
ATOM     13  H   SER     3      26.848  28.467  28.826  0.2719 0.6000
ATOM     13  HA  SER     3      25.033  26.163  28.896  0.0843 1.3870
ATOM     13  HB2 SER     3      24.667  28.907  29.866  0.0352 1.3870
ATOM     13  HB3 SER     3      23.737  27.639  30.306  0.0352 1.3870
ATOM     13  HG  SER     3      26.135  26.859  30.756  0.4275 0.0000
ATOM     19  N   GLU     4      24.356  28.363  26.737 -0.5163 1.8240
ATOM     20  CA  GLU     4      23.370  28.880  25.827  0.0397 1.9080
ATOM     21  C   GLU     4      23.055  27.958  24.640  0.5366 1.9080
ATOM     22  O   GLU     4      23.937  27.450  23.989 -0.5819 1.6612
ATOM     23  CB  GLU     4      23.907  30.215  25.273  0.0560 1.9080
ATOM     24  CG  GLU     4      22.953  30.893  24.324  0.0136 1.9080
ATOM     25  CD  GLU     4      23.186  32.384  24.168  0.8054 1.9080
ATOM     26  OE1 GLU     4      23.239  33.074  25.208 -0.8188 1.6612
ATOM     27  OE2 GLU     4      23.290  32.799  23.000 -0.8188 1.6612
ATOM     19  H   GLU     4      25.367  28.594  26.697  0.2936 0.6000
ATOM     19  HA  GLU     4      22.499  29.071  26.328  0.1105 1.3870
ATOM     19  HB2 GLU     4      24.053  30.810  26.040 -0.0173 1.4870
ATOM     19  HB3 GLU     4      24.735  30.016  24.787 -0.0173 1.4870
ATOM     19  HG2 GLU     4      23.057  30.484  23.428 -0.0425 1.4870
ATOM     19  HG3 GLU     4      22.031  30.775  24.664 -0.0425 1.4870
sobolevnrm commented 3 years ago

Can you please provide the file that caused this problem? Thanks.

dvdesolve commented 3 years ago

pdb2pqr30 --ff=AMBER --ffout=AMBER --titration-state-method=propka --with-ph=7.5 holoenzyme.pdb holoenzyme_H.pqr

Input: holoenzyme.pdb.txt (renamed due to GH limitations) Output: holoenzyme_H.pqr.txt (renamed due to GH limitations) Log: pdb2pqr.log

Calcium is added to the dat/AMBER.DAT by me:

CA  CA  2.000000    1.6490  Ca2+

Please notice that I was forced to apply fix as described in #131 because otherwise a bunch of warnings were generated in output

sobolevnrm commented 3 years ago

FWIW, this problem doesn't happen with the server which means it must be a bug I've introduced since then -- I can reproduce it with the head of the master branch.