For my Bachelor’s thesis, I am trying to simulate DNA on a diamond surface, but pdb2gmx can not deal with the diamond surface and with the bond between the DNA and the diamond. And there is no .pdb file available anyway. So I have to build the topology without pdb2gmx.
I am having trouble calculating the partial charges for the topology.
Is there any way to assign charges automatically without pdb2gmx?
What will Gromacs do if I set all charges to 0?
Do you think that using this tool to assign charges for my whole system is a good idea?
At the moment, only the DNA part of my system has charges because I was able to use pdb2gmx to create its topology.
I am very grateful for any comments. Sorry for the maybe amateur question.
No, GROMACS has no built-in parametrization abilities.
Your topology will have no charges on this species and will be physically invalid.
Are its charge calculation methods compatible with the parent force field you are using for DNA? Force field parametrization is an extremely difficult topic and you have to be sure that any topology you generate is derived in the same manner (same QM level of theory, same target data, etc) as the existing parameters. Otherwise, all you’ve got is a random-number generator rather than a predictive simulation.