[gmx-users] GBSA parameters

[Jack Shepherd]

Dear all,

I am interested in running an implicit solvent DNA simulation. Attempting
to run grompp with gbsa turned on resulted in the error message

GB parameter(s) missing or negative for atom type 'OS'

GB parameter(s) missing or negative for atom type 'H2'

GB parameter(s) missing or negative for atom type 'N*'

GB parameter(s) missing or negative for atom type 'CK'

GB parameter(s) missing or negative for atom type 'P'

-------------------------------------------------------
Program:     gmx grompp, version 2018.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1335)

Fatal error:
Can't do GB electrostatics; the implicit_genborn_params section of the
forcefield is missing parameters for 5 atomtypes or they might be negative.

The PDB was generated with nab from AmberTools 16.

Clearly I need to add the GBSA values to /usr/share/...../gbsa.itp. My
guess is that I can copy the hydrogen values from the other hydrogens as
they are all the same, and choose an appropriate line to copy for the O,
N*, and CK.

Can anyone point to something which will help me with which to copy and how
to add the missing P values? Or a download I may have missed somewhere
along the way?

Thanks all in advance

jack