pdb2pqr
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Electrostatics
naming inconsistency with CHARMM
I am trying to get the pka for 1tiv.pdb and write the output using the CHARMM naming scheme. It appears that the residues names are inconsistently named. Namely, pdb2pqr 1tiv.pdb 1tiv.pqr --ffout=CHARMM --titration-state-method=propka --with-ph=3 produces a 1tiv.pqr file that name GLU as GLUP. Can you please help?
Thanks, Nihit
Running pdb2pqr 1tiv.pdb 1tiv.pqr --ffout=CHARMM --titration-state-method=propka --with-ph=2 generates protonated versions of ASP and GLU with inconsistent residue names for atoms within a single residue. For example:
ATOM 20 N ASP 2 -9.450 4.065 3.037 -0.4000 1.5000
ATOM 21 CA ASP 2 -9.506 5.204 4.058 -0.0000 2.0000
ATOM 22 C ASP 2 -8.836 4.814 5.409 0.5500 1.7000
ATOM 23 O ASP 2 -7.935 5.518 5.829 -0.5500 1.4000
ATOM 24 CB ASPP 2 -10.936 5.748 4.325 0.0000 2.0000
ATOM 25 CG ASPP 2 -10.862 6.973 5.243 0.5500 1.7000
ATOM 26 OD2ASPP 2 -10.646 8.053 4.737 -0.4900 1.4000
ATOM 27 OD1ASPP 2 -11.012 6.802 6.442 -0.4950 1.4000
ATOM 28 HN ASP 2 -8.535 3.765 2.621 0.4000 1.0000
ATOM 29 HA ASP 2 -8.969 5.952 3.664 0.0000 0.0000
ATOM 30 HB2ASPP 2 -11.320 6.017 3.467 0.0000 0.0000
ATOM 31 HB1 ASP 2 -11.446 5.046 4.773 0.0000 0.0000
ATOM 32 HD2ASPP 2 -10.501 8.135 3.729 0.4350 1.0000
and
ATOM 123 N GLU 9 4.581 2.477 6.758 -0.4000 1.5000
ATOM 124 CA GLU 9 5.953 2.181 7.229 -0.0000 2.0000
ATOM 125 C GLU 9 6.378 0.908 6.472 0.5500 1.7000
ATOM 126 O GLU 9 7.243 0.988 5.617 -0.5500 1.4000
ATOM 127 CB GLU 9 6.009 2.004 8.761 0.0000 2.0000
ATOM 128 CG GLUP 9 7.097 2.916 9.346 0.0000 2.0000
ATOM 129 CD GLUP 9 8.476 2.264 9.203 0.5500 1.7000
ATOM 130 OE2GLUP 9 9.081 2.423 8.156 -0.4900 1.4000
ATOM 131 OE1GLUP 9 8.904 1.621 10.146 -0.4950 1.4000
ATOM 132 HN GLU 9 3.958 1.705 6.379 0.4000 1.0000
ATOM 133 HA GLU 9 6.552 2.920 6.995 0.0000 0.0000
ATOM 134 HB2 GLU 9 5.162 2.288 9.122 0.0000 0.0000
ATOM 135 HB1 GLU 9 6.260 1.093 8.945 0.0000 0.0000
ATOM 136 HG2GLUP 9 7.108 3.742 8.837 0.0000 0.0000
ATOM 137 HG1 GLU 9 6.923 3.030 10.294 0.0000 0.0000
ATOM 138 HE2GLUP 9 10.011 1.979 8.057 0.4350 1.0000
Additionally, the C-terminal GLU is named GLU rather than GLUP and the GLU sidechain is protonated but the C-terminus is not.
The protonated version of HIS appears to be named correctly.
PDB2PQR appears to be treating these changes like CHARMM patches (e.g., see https://github.com/openmm/openmmforcefields/issues/22) rather than renaming full residues. This is done in various places in the code by an if statement applied to atom name:
- GLY to GLYP N-terminus patch: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L726
- PRO to PROP N-terminus patch: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L742
- GLU to GLUP patch: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L829 and https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L843
- ASP to ASPP patch: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L864 and https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L878
- CYS disulfide DISU patch: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L808 and https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L811
However, I don't think this is the desired behavior; I can't think of a good reason for it. It is likely a bug that came from an over-literal interpretation of the CHARMM forcefield files during initial implementation. I'm going to change it to rename the full residue unless @orbeckst or @speleo3 can think of a reason I should keep it.
Thanks!
Actually, it looks like this code is never used. The get_charmm_params code is only called from get_params1 which is never called: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L363
The input parameter file must be incomplete. Some debugging information can be obtained by dumping the residue map immediately after this line: https://github.com/Electrostatics/pdb2pqr/blob/8db8d949ec31c7544d87417a152597bddf808b6e/pdb2pqr/forcefield.py#L197
The GLU-related items from this dump are:
GLU
GLU: N: N:
Charge: -0.4700
Radius: 1.8500,HN: HN:
Charge: 0.3100
Radius: 0.2245,CA: CA:
Charge: 0.0700
Radius: 2.2750,HA: HA:
Charge: 0.0900
Radius: 1.3200,CB: CB:
Charge: -0.1800
Radius: 2.1750,HB1: HB1:
Charge: 0.0900
Radius: 1.3200,HB2: HB2:
Charge: 0.0900
Radius: 1.3200,CG: CG:
Charge: -0.2800
Radius: 2.1750,HG1: HG1:
Charge: 0.0900
Radius: 1.3200,HG2: HG2:
Charge: 0.0900
Radius: 1.3200,CD: CD:
Charge: 0.6200
Radius: 2.0000,OE1: OE1:
Charge: -0.7600
Radius: 1.7000,OE2: OE2:
Charge: -0.7600
Radius: 1.7000,C: C:
Charge: 0.5100
Radius: 2.0000,O: O:
Charge: -0.5100
Radius: 1.7000
GLUP
GLUP: CG: CG:
Charge: -0.2100
Radius: 2.1750,HG1: HG1:
Charge: 0.0900
Radius: 1.3200,HG2: HG2:
Charge: 0.0900
Radius: 1.3200,CD: CD:
Charge: 0.7500
Radius: 2.0000,OE1: OE1:
Charge: -0.5500
Radius: 1.7000,OE2: OE2:
Charge: -0.6100
Radius: 1.7700,HE2: HE2:
Charge: 0.4400
Radius: 0.2245
Unfortunately, it looks like GLUP is missing some atoms.
This will be easier to fix if we don't have to deal with XML-format data files; it might finally be time to replace those.
- [ ] Fix #367