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Electrostatics / pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Naming of hydrogen atoms #208

Closed boristim66 closed 3 years ago

boristim66 commented 3 years ago

I found that for added hydrogen atoms, if there are two, their numbering begins with "2", regardless of the chosen scheme of naming atoms.
I have never met with such a scheme of names in moldinamics before. For Gromacs, such names create great difficulties. Is that a feature or a bug?

ATOM 1 N ASP A 5 74.598 95.955 67.868 0.0782 1.8240 ATOM 2 CA ASP A 5 74.693 95.148 66.625 0.0292 1.9080 ATOM 3 C ASP A 5 74.184 93.718 66.822 0.5621 1.9080 ATOM 4 O ASP A 5 74.761 92.941 67.592 -0.5889 1.6612 ATOM 5 CB ASP A 5 76.141 95.128 66.151 -0.0235 1.9080 ATOM 6 CG ASP A 5 76.607 96.482 65.672 0.8194 1.9080 ATOM 7 OD1 ASP A 5 77.755 96.592 65.203 -0.8084 1.6612 ATOM 8 OD2 ASP A 5 75.820 97.442 65.759 -0.8084 1.6612 ATOM 9 H1 ASP A 5 73.883 95.578 68.452 0.2200 0.6000 ATOM 10 HA ASP A 5 74.090 95.589 65.948 0.1141 1.1000 ATOM 11 HB2 ASP A 5 76.711 94.843 66.913 -0.0169 1.4870 ATOM 12 HB3 ASP A 5 76.212 94.480 65.402 -0.0169 1.4870 ATOM 13 H2 ASP A 5 75.473 95.926 68.347 0.2200 0.6000 ATOM 14 H3 ASP A 5 74.375 96.899 67.632 0.2200 0.6000

AMBER naming for this terminal residue:

[ NASP ] [ atoms ] N N3 0.07820 1 H1 H 0.22000 2 H2 H 0.22000 3 H3 H 0.22000 4 CA CT 0.02920 5 HA HP 0.11410 6 CB CT -0.02350 7 HB1 HC -0.01690 8 HB2 HC -0.01690 9 CG C 0.81940 10 OD1 O2 -0.80840 11 OD2 O2 -0.80840 12 C C 0.56210 13 O O -0.58890 14

boristim66 commented 3 years ago

I looked at the AMBER parameters, indeed, the names are such, beginning with "2." It seems that I will have to make my own DAT file for use with Gromacs. I'm closing this issue.