GROMACS version: 2020.1
GROMACS modification: No
I am doing simulations of a protein nanopore-membrane system, and would like to create electrostatic potential maps using VMD pmepot plugin. For this, I need a topology file containing atom charges informations, often a .pqr file. I tried to generate it using -grasp command of gmx trjconv, but the results are wrong (huge inconsistent) values and after discussions with members of the lab I am doing this project in, they told me that they had the same issue and used NAMD to create these (charges informations are stored directly is the topology file). However, I want to stick with gromacs since all my simulations are already done! Is there a way where I can get such file using gromacs? After searching over the internet, I could not find a right way to do it!