[gmx-users] Grompp error

Hanin Omar hanin_omar85 at yahoo.com
Sun Mar 24 17:41:34 CET 2019


Hello everyone
I am using gromacs version 2019, and I want to add dihedral restraint to the backbone of the last helix in my protein in my simulation, however grompp gives me this error
ERROR 1 [file D2-TorisionRes.itp, line 5]:
  Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest.
  (after the function type).

from my understanding this means that i am missing one feild in my restraint file, can someone tell me what is it?This is the content of my D2-TorisionRes.itp file :[ dihedral_restraints ]
;For the second domain starting from residue 74
; ai        aj     ak      al   type   label   phi   dphi   kfac   power
;  C(i-1)   Ni  C-alphai   Ci     1        1   value   0      1.0    2.0  
   1159    1174  1175     1176    1        1  -70.2    0      1.0    2.0  ;res 74
   1176    1186  1187     1188    1        1  -91.0    0      1.0    2.0  ;res 75
   1188    1205  1206     1207    1        1  -53.4    0      1.0    2.0  ;res 76

and in my topology file i added this line after the molecule:; Include Dihedral restraint file
#ifdef DIHRE
#include "D2-TorisionRes.itp"
#endif

and in my mdp file i used:define           = -DDIHRE


is my implementation of the dihedral restraint correct so far? also do i have to include them in all the equiliberation steps?
THank you for the help

Sent from my iPhone


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