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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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AMBER has H atom in CYM residue #197

Closed stefdoerr closed 3 years ago

stefdoerr commented 3 years ago

Looking at the AMBER forcefield I cannot find the HN atom in the CYM residue definition. This was an older patch we had applied to fix these cases so I don't have an example ready but you can look at the AMBER lib files

!entry.CYM.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
    "N"     "N"     0   1   131072   1   7 -1.02108
    "H"     "H"     0   1   131072   2   1  0.39367
    "CA"    "TM"    0   1   131072   3   6  1.11287
    "HA"    "H1"    0   1   131072   4   1 -0.19174
    "CB"    "2C"    0   1   131072   5   6 -0.19492
    "HB3"   "H1"    0   1   131072   6   1  0.06223
    "HB2"   "H1"    0   1   131072   7   1  0.06223
    "SG"    "SH"    0   1   131072   8  16 -0.85397
    "C"     "C"     0   1   131072   9   6  0.09421
    "O"     "OD"    0   1   131072  10   8 -0.46350