[gmx-users] proper and improper dihedrals in topology file from other ff

[라지브간디]

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? 
>