Dear Justin,
I have looked over the chapter 5 and had difficult to understand the interpreting the LJ 6-12 value for my ligand file. I just want to give particular value only for NO ligand, therefore i want to know how do i give them in topology file? As you already mentioned that I should change them in [atomtypes] else special interaction in [nonbond_params] in ffnonboneded.itp file. If i do that, I wonder it could be giving this value for my protein too? What i want in here is, how do i specify the value only for NO ligand in .itp file which is created by pdb2gmx. I believe, the [pairs] column in the .itp also only for 1-4 LJ value? Thanks in advance. Dear gmx, > > I want set the particular value of lennard jones 6-12 for NO ligand for my > simulation. I believe it has be mentioned in topology file created by force > field. My questions is how to set these value in topology which created by > CHARMM 27 ff? > The directives in ffnonbonded.itp control these interactions. You can either modify that file (or better, a local copy in case something goes wrong) or just add the relevant directives in your topology directly (new atom types in [atomtypes] or special interactions for existing atom types in [nonbond_params]). See Chapter 5 of the manual. -Justin
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