Dihedral restraint error

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
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After i create the [Dihedral restraint] and add it to my top file , i got the following error.
This is my Dihedral restraint file
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
;DVal-2
; phi C’(n-1) - N - CA - C’
21 23 25 37 1 1 81 0 1 2
; psi N - CA - C’ - N(n+1)
23 25 37 39 1 1 -152 0 1 2
;Val-3
; phi C’(n-1) - N - CA - C’
37 39 41 53 1 1 -144 0 1 2
; psi N - CA - C’ - N(n+1)
39 41 53 55 1 1 123 0 1 2
;DVal-4
; phi C’(n-1) - N - CA - C’
53 55 57 69 1 1 105 0 1 2
; psi N - CA - C’ - N(n+1)
55 57 69 71 1 1 -156 0 1 2
;Val-5
; phi C’(n-1) - N - CA - C’
69 71 73 85 1 1 -145 0 1 2
; psi N - CA - C’ - N(n+1)
71 73 85 87 1 1 101 0 1 2
;DVAL-6
; phi C’(n-1) - N - CA - C’
85 87 89 101 1 1 121 0 1 2
; psi N - CA - C’ - N(n+1)
87 89 101 103 1 1 -155 0 1 2
;VAL-7
; phi C’(n-1) - N - CA - C’
101 103 105 117 1 1 -149 0 1 2
; psi N - CA - C’ - N(n+1)
103 105 117 119 1 1 100 0 1 2

GROMACS: gmx grompp, VERSION 5.1.5
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx grompp -f step6.0_minimization.mdp -o step6.0_minimization.tpr -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
Setting the LD random seed to 4121815648
Generated 465 of the 465 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 0 of the 465 1-4 parameter combinations

Program gmx grompp, VERSION 5.1.5
Source code file: /home/rsr/Downloads/gromacs-5.1.5/src/gromacs/gmxpreprocess/toppush.c, line: 1949

Fatal error:
Incorrect number of parameters - found 5, expected 3 or 6 for Dih. Rest…
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

2

Hi,
The program is expecting 6 parameters but it finds only 5. Have you try to reformat your directive [ dihedral_restraints ] or check the line that causes the error.
Best regards
Alessandra

3

After I exclude the label and power I didn’t face any error ,is it fine to exclude label and power ?

4

Hi,
I see that you are using GROMACS 5.1. There may be difference with the current version, I do not recall. You can check if the restrains you apply are what you want by looking GROMACS 5.1 manual- Chapter 4 and table 5.5

\Alesssandra

5

I am a tyro in distance restraining hence i am facing difficulties in making the file for it as i dont know how to reckon the value of ro,r1etc parameter.

What i have is just distance between two atom but i dont know how to get the value of r0, r1 etc for distance restraint.

//Rakesh