GROMACS version:
GROMACS modification: Yes/No
Here post your question: I am trying to build a biphasic system of cyclohexane-water and place peptide in it (as in tutorial). After simulating cyclohexane box, extending it and adding protein followed by solvation and adding ions, when I am moving on to energy minimisation, I am getting the following error
I tried increasing the box size too, but cannot resolve the error. As it says the error is with cyclohexane, but I obtained the cyclohexane files from charm GUI (not CGenff server), as I am using charmm36 forcefield. I have attached all files for cyclohexane and em.mdp file too.
CYHE.pdb -
REMARK GENERATE LIGAND
REMARK DATE: 5/ 9/24 1:35:18 CREATED BY USER: apache
ATOM 1 C1 CYH C 1 -0.104 -0.151 0.004 1.00 0.00 CYHE
ATOM 2 H11 CYH C 1 -0.360 -0.773 0.890 1.00 0.00 CYHE
ATOM 3 H12 CYH C 1 -0.603 -0.610 -0.878 1.00 0.00 CYHE
ATOM 4 C2 CYH C 1 1.425 -0.201 -0.181 1.00 0.00 CYHE
ATOM 5 H21 CYH C 1 1.686 -1.075 -0.817 1.00 0.00 CYHE
ATOM 6 H22 CYH C 1 1.899 -0.356 0.814 1.00 0.00 CYHE
ATOM 7 C3 CYH C 1 2.013 1.077 -0.795 1.00 0.00 CYHE
ATOM 8 H31 CYH C 1 1.628 1.168 -1.835 1.00 0.00 CYHE
ATOM 9 H32 CYH C 1 3.120 0.989 -0.852 1.00 0.00 CYHE
ATOM 10 C4 CYH C 1 1.649 2.358 -0.021 1.00 0.00 CYHE
ATOM 11 H41 CYH C 1 1.585 3.192 -0.754 1.00 0.00 CYHE
ATOM 12 H42 CYH C 1 2.463 2.608 0.695 1.00 0.00 CYHE
ATOM 13 C5 CYH C 1 0.333 2.265 0.774 1.00 0.00 CYHE
ATOM 14 H51 CYH C 1 -0.130 3.275 0.831 1.00 0.00 CYHE
ATOM 15 H52 CYH C 1 0.567 1.944 1.814 1.00 0.00 CYHE
ATOM 16 C6 CYH C 1 -0.674 1.269 0.184 1.00 0.00 CYHE
ATOM 17 H61 CYH C 1 -1.575 1.219 0.834 1.00 0.00 CYHE
ATOM 18 H62 CYH C 1 -0.996 1.652 -0.809 1.00 0.00 CYHE
TER 19 CYHE 1
END
CYHE.itp -
;;
;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
;;
;; psf2itp_mol.py
;;
;; Correspondance:
;; jul316@lehigh.edu or wonpil@lehigh.edu
;;
;; GROMACS topology file for CYHE
;;
[ moleculetype ]
; name nrexcl
CYHE 3
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CG321 1 CYHE C1 1 -0.180 12.0110 ; qtot -0.180
2 HGA2 1 CYHE H11 2 0.090 1.0080 ; qtot -0.090
3 HGA2 1 CYHE H12 3 0.090 1.0080 ; qtot 0.000
4 CG321 1 CYHE C2 4 -0.180 12.0110 ; qtot -0.180
5 HGA2 1 CYHE H21 5 0.090 1.0080 ; qtot -0.090
6 HGA2 1 CYHE H22 6 0.090 1.0080 ; qtot 0.000
7 CG321 1 CYHE C3 7 -0.180 12.0110 ; qtot -0.180
8 HGA2 1 CYHE H31 8 0.090 1.0080 ; qtot -0.090
9 HGA2 1 CYHE H32 9 0.090 1.0080 ; qtot 0.000
10 CG321 1 CYHE C4 10 -0.180 12.0110 ; qtot -0.180
11 HGA2 1 CYHE H41 11 0.090 1.0080 ; qtot -0.090
12 HGA2 1 CYHE H42 12 0.090 1.0080 ; qtot 0.000
13 CG321 1 CYHE C5 13 -0.180 12.0110 ; qtot -0.180
14 HGA2 1 CYHE H51 14 0.090 1.0080 ; qtot -0.090
15 HGA2 1 CYHE H52 15 0.090 1.0080 ; qtot 0.000
16 CG321 1 CYHE C6 16 -0.180 12.0110 ; qtot -0.180
17 HGA2 1 CYHE H61 17 0.090 1.0080 ; qtot -0.090
18 HGA2 1 CYHE H62 18 0.090 1.0080 ; qtot 0.000
[ bonds ]
; ai aj funct b0 Kb
1 2 1
1 3 1
1 4 1
1 16 1
4 5 1
4 6 1
4 7 1
7 8 1
7 9 1
7 10 1
10 11 1
10 12 1
10 13 1
13 14 1
13 15 1
13 16 1
16 17 1
16 18 1
[ pairs ]
; ai aj funct c6 c12
1 8 1
1 9 1
1 10 1
1 14 1
1 15 1
2 5 1
2 6 1
2 7 1
2 13 1
2 17 1
2 18 1
3 5 1
3 6 1
3 7 1
3 13 1
3 17 1
3 18 1
4 11 1
4 12 1
4 13 1
4 17 1
4 18 1
5 8 1
5 9 1
5 10 1
5 16 1
6 8 1
6 9 1
6 10 1
6 16 1
7 14 1
7 15 1
7 16 1
8 11 1
8 12 1
8 13 1
9 11 1
9 12 1
9 13 1
10 17 1
10 18 1
11 14 1
11 15 1
11 16 1
12 14 1
12 15 1
12 16 1
14 17 1
14 18 1
15 17 1
15 18 1
[ angles ]
; ai aj ak funct th0 cth S0 Kub
2 1 3 5
2 1 4 5
2 1 16 5
3 1 4 5
3 1 16 5
4 1 16 5
1 4 5 5
1 4 6 5
1 4 7 5
5 4 6 5
5 4 7 5
6 4 7 5
4 7 8 5
4 7 9 5
4 7 10 5
8 7 9 5
8 7 10 5
9 7 10 5
7 10 11 5
7 10 12 5
7 10 13 5
11 10 12 5
11 10 13 5
12 10 13 5
10 13 14 5
10 13 15 5
10 13 16 5
14 13 15 5
14 13 16 5
15 13 16 5
1 16 13 5
1 16 17 5
1 16 18 5
13 16 17 5
13 16 18 5
17 16 18 5
[ dihedrals ]
; ai aj ak al funct phi0 cp mult
2 1 4 5 9
2 1 4 6 9
2 1 4 7 9
3 1 4 5 9
3 1 4 6 9
3 1 4 7 9
2 1 16 13 9
2 1 16 17 9
2 1 16 18 9
3 1 16 13 9
3 1 16 17 9
3 1 16 18 9
4 1 16 13 9
4 1 16 17 9
4 1 16 18 9
5 4 1 16 9
6 4 1 16 9
7 4 1 16 9
1 4 7 8 9
1 4 7 9 9
1 4 7 10 9
5 4 7 8 9
5 4 7 9 9
5 4 7 10 9
6 4 7 8 9
6 4 7 9 9
6 4 7 10 9
4 7 10 11 9
4 7 10 12 9
4 7 10 13 9
8 7 10 11 9
8 7 10 12 9
8 7 10 13 9
9 7 10 11 9
9 7 10 12 9
9 7 10 13 9
7 10 13 14 9
7 10 13 15 9
7 10 13 16 9
11 10 13 14 9
11 10 13 15 9
11 10 13 16 9
12 10 13 14 9
12 10 13 15 9
12 10 13 16 9
10 13 16 17 9
10 13 16 18 9
14 13 16 17 9
14 13 16 18 9
15 13 16 17 9
15 13 16 18 9
1 16 13 10 9
1 16 13 14 9
1 16 13 15 9
(About the inconsistent naming of the molecule, when I changed it in pdb file, the structure seemed different in vmd, so changed the name in itp and topology files, and it worked fine)
minim.mdp-
; LINES STARTING WITH ‘;’ ARE COMMENTS
title = Minimization ; Title of run
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; long range electrostatic cut-off
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
DispCorr = no
Note : For equilibrating cyclohexane box, I used C-rescale barostat and V-rescale thermostat with tau_p = 5, and tau_t = 1. I used cubic box (888) for cyclohexane. Everything worked fine for cyclohexane box, but on extending, placing protein and solvation , on energy minimization , the error shows up everytime and energy minimization is not even starting. (I did not use posre for cyclohexane).
Kindly anyone help me with this, as it’s very very urgent for my project.
