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mms-fcul / PypKa

A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
https://pypka.readthedocs.io/en/latest/
GNU Lesser General Public License v3.0
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Dealing with Multiple Chains without the chain index #4

Closed shaoqx closed 4 years ago

shaoqx commented 4 years ago

It seems only the last chain is calculated, or at least only the last chain is printed. My format is still the Amber format that uses a TER to separate those chains and there’s no chain index in the lines, like this:

ATOM      1  N   GLY     1      12.837  -6.638  21.081  1.00  0.00
...
ATOM    452  O   ILE    30      -3.827  -8.956  -6.496  1.00  0.00
TER
ATOM    453  N   ARG    31      -3.139 -10.540  -7.939  1.00  0.00
ATOM    454  H   ARG    31      -2.449 -11.198  -8.164  1.00  0.00
ATOM    455  CA  ARG    31      -4.296 -10.383  -8.812  1.00  0.00
...
TER
END
shaoqx commented 4 years ago

The ffinput has set to AMBER in this case.

pedrishi commented 4 years ago

Hi again @shaoqx !

In order to use multiple chains, the PDB has to be marked explicitly with the chain identifier (column 22).

shaoqx commented 4 years ago

I see, so the pdb should be reformed before determining the pKa. Thank you!