Copy atomtype to new one with the same bonded interactions

User discussions
1

Dear all,

I need to add new atom types to my topology file for only some atoms and only in some specific residues (eg. adenine 1 but not adenine 2). Then, I need to modify their LJ parameters but I want to keep bond/angle/torsion parameters unchanged. The way to do it is to rename the atomtypes of atoms of interest and then define these new atomtypes with the unchanged mass/charge and changed LJ. Then, I need to define also all bond/angle/torsion parameters by manually copying all the entries that include the original atomtypes and rename the atomtypes there. My question is whether there is any easier/automatic way to do this? To just change LJ params of specific atoms without affecting their other parameters or to copy the atomtypes into new ones and transfer all the parameters automatically? Some grompp functionality or tool?

Thank you,
Pavlina

2

If you change LJ terms and try to apply the same dihedrals, they likely won’t work. Dihedrals are fixes for incorrect modeling of 1-4 LJ and electrostatic terms. So if you change these, you need to reparametrize the dihedrals.