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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
http://www.poissonboltzmann.org/
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Terminal histidine protonation issues #257

Closed stefdoerr closed 2 years ago

stefdoerr commented 2 years ago

Seems like pdb2pqr has issues with terminal histidines. While it does protonate the histidine correctly removing the HE2 atom it does not rename it to HID. Instead it keeps it as HIS which causes issues in teLeap since AMBER does not like HIS residues with a HD1 atom. The rest of non-terminal histidines are correctly renamed.

IL2BG_wt.zip

pdb2pqr30 --ff PARSE --ffout AMBER ./IL2BG_wt.pdb ./IL2BG_wt.pqr

[...]
ATOM   3279  HA2 GLY   208     -20.236   5.055  25.169  0.0000 0.0000
ATOM   3280  HA3 GLY   208     -19.995   3.608  25.885  0.0000 0.0000
ATOM   3281  N   HIS   209     -22.647   3.943  25.586 -0.4000 1.5000
ATOM   3282  CA  HIS   209     -24.079   3.825  25.905 -0.0000 2.0000
ATOM   3283  C   HIS   209     -24.547   2.387  26.129  0.1000 1.7000
ATOM   3284  O   HIS   209     -23.728   1.438  26.038 -0.5500 1.4000
ATOM   3285  CB  HIS   209     -24.944   4.503  24.836  0.1250 2.0000
ATOM   3286  CG  HIS   209     -24.988   5.997  24.951 -0.1250 1.7000
ATOM   3287  OXT HIS   209     -25.652   1.939  26.402 -0.5500 1.4000
ATOM   3288  H   HIS   209     -22.231   3.606  24.703  0.4000 1.0000
ATOM   3289  HA  HIS   209     -24.255   4.352  26.757  0.0000 0.0000
ATOM   3290  HB2 HIS   209     -24.584   4.266  23.927  0.0000 0.0000
ATOM   3291  HB3 HIS   209     -25.884   4.153  24.908  0.0000 0.0000
ATOM   3292  ND1 HIS   209     -26.004   6.664  25.606 -0.4000 1.5000
ATOM   3293  CD2 HIS   209     -24.137   6.952  24.503  0.1550 1.7000
ATOM   3294  CE1 HIS   209     -25.778   7.965  25.555  0.1550 1.7000
ATOM   3295  NE2 HIS   209     -24.652   8.167  24.889 -0.5600 1.5000
ATOM   3296  HD1 HIS   209     -26.786   6.227  26.049  0.4000 1.0000
ATOM   3297  HD2 HIS   209     -23.297   6.804  23.990  0.1250 1.0000
ATOM   3298  HE1 HIS   209     -26.355   8.674  25.948  0.1250 1.0000
TER
sobolevnrm commented 2 years ago

Hi @stefdoerr --

Is this the same issue as #245 ? Does the example there reproduce the error for you?

Thank you,

Nathan

stefdoerr commented 2 years ago

Oh yes indeed it's a duplicate. I'll close it