On Saturday, March 23, 2013, 라지브간디 wrote: > 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. > > > Simulations of heme-containing proteins are fairly common. Certainly someone will have published a complete parameter set. Mixing force fields and ignoring energy terms are not sensible.
-Justin > > > 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 ? > > > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
