Dear 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? Every force field has small differences in format. Look at ffbonded.itp for 43A1 and you will see #define statements that correspond to bonds (gb_*), angles (ga_*), etc. Those macros just mean "substitute this information here." It's shorthand. So either you can introduce a new definition in ffbonded.itp or just type the parameters in manually according to the format specified in the manual. -Justin Dear gmx users, > > > I am MD simulation for heme ligated protein where i given all bond and angle, > dihedral information in topology file created by pd2gmx ( gromos43a1). > > > However, i do not know how to interpret the proper and improper dihedrals in > topology file? I have looked over the .rtp file and found that gromos > mentioned like > > example: > > > [ impropers ] > ; ai aj ak al gromos type > C2 N1 N3 NA2 gi_1 > NA2 HA21 HA22 C2 gi_1 > N3 C2 C4 HA3 gi_1 > > > But the the parameter I use from literature where its in charmm and amber > format as they mentioned the torsions like following way. > > > Improper > CPB-X-X-CR1E 90.0 0.0 > CC - X-X-NB 18.3 0.0 > > > ...............etc > > > How do i use this improper to utilize in gromos? >
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