GROMACS version: 2020.1
GROMACS modification: No
Dear Gromacs User Forum,
I am new to Gromacs.
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.
Thank you & Best Regards,