Thanks for your reply. Except charmm27 in gmx, all the ff fails to describe the angle, bonds and dihedral of heme ligated proteins. Also, Chamm27 also couldnt do for heme interacts with histidine part. Hence I've utilized the parameter details from articles. Only I am missing how do I describe the torsion angle details to this particular heme ligand part. Is that okay if I avoid the torsion ?
Hope you understand what I mean in here. > Different force fields derive and implement parameters in different ways. > Hence why it makes no sense to try to combine them. > 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 ). If you're doing this, you're creating a hybrid force field that makes no sense. There are parameters for heme within Gromos96 already; why are you making these modifications? > 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 ? >
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