[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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