Dear Justin, Actually I've manually added the heme -ligand parameters details such as bond, angle and dihedral to my topology created by pdb2gmx via gromos43a1. ( Those manually added parameters details are taken from charmm and amber ff, which are available in some published articles ). I confused while interpreting the improper values from those published article where they both shown (amber and charmm) improper in X (generic indicator) way, whereas the gromos improper values for atoms are in direct way by not using X generic indicator.
Is that improper details are important for heme-ligand case ? If so, how do I make them favor to gromos by this article values ? Thanks in advance I don't understand entirely what you're trying to do. You shouldn't be trying to implement CHARMM or AMBER parameters in Gromos. X is a generic indicator signifying atoms Justin. > I got understand the gromos ff improper style. however, what i am asking here > is how would i use the charmm/amber improper from literuatre where they > indicate the improper in this was ( something X-X) > > > > > Improper >> CPB-X-X-CR1E 90.0 0.0 >> CC - X-X-NB 18.3 0.0 >> > > > > > > > What X shows here and how do i use this in gromos format way? > >
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