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? Thanks in advance.
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