[gmx-users] Trouble with restrained dihedrals

[Marko Petrovic]

Bottom post:
On 16 Apr 2020, at 08:56, Marko Petrovic <marko at kth.se<mailto:marko at kth.se>> wrote:

Hello

I'm trying to run an Energy Minimisation run while restraining phi and psi of the central alanine of an alanine dipeptide in vacuum. Hopefully it won't make a difference if I run a EM equilibration or other run for this error/concept since I am trying to create a script for creating/updating the necessary files for several different simulation runs.

The error message:
ERROR 1 [file cv_restraints.itp, line 3]:
  Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest.
  (after the function type).

The .itp file contents:
[ dihedral_restraints ]
; ai   aj   ak   al  type  label  phi  dphi  kfac  power
         5         7         9        15         1         1   -67.652   0   1   2
         7         9        15        17         1         1    59.806   0   1   2

Other possibly relevant file snippets:
.mdp file define row (1st row):
define                    = -DPOSRES_CV

topol.top ifdef statement (last in file):
#ifdef POSRES_CV
#include "cv_restraints.itp"
#endif

I hope this is the info needed to easily see what I've done wrong. (Also info on how to interpret the error message would be nice, like which 5 parameters the software found and how it coun'ts parameters so I can get them to 3 or 6 if the problem is in the .utp file)

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology

Also, the most up to date documentation on dihedral restraints I easily found was:
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints

Is this still relevant?

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology