GROMACS version:
GROMACS modification: Yes/No
Here post your question
Hey, I have attached the files I used for creating the .pdb file that I will be using for MD calculation at Gromacs. Can you kindly check for errors? Because I have tried everything I can, and still I find errors in labeling atoms.
electrode.pdb file
HEADER Graphene
COMPND
SOURCE
HETATM 1 C1 CG 1 0.002 1.419 7.000 1.00 1.00 C
HETATM 2 C2 CG 1 1.228 0.711 7.000 1.00 1.00 C
HETATM 3 C3 CG 1 -1.228 3.550 7.000 1.00 1.00 C
HETATM 4 C4 CG 1 -0.002 2.842 7.000 1.00 1.00 C
HETATM 5 C5 CG 1 -2.458 5.680 7.000 1.00 1.00 C
HETATM 6 C6 CG 1 -1.232 4.972 7.000 1.00 1.00 C
HETATM 7 C7 CG 1 -3.688 7.810 7.000 1.00 1.00 C
HETATM 8 C8 CG 1 -2.462 7.103 7.000 1.00 1.00 C
HETATM 9 C9 CG 1 2.462 1.419 7.000 1.00 1.00 C
HETATM 10 C10 CG 1 3.688 0.711 7.000 1.00 1.00 C
HETATM 11 C11 CG 1 1.232 3.550 7.000 1.00 1.00 C
HETATM 12 C12 CG 1 2.458 2.842 7.000 1.00 1.00 C
HETATM 13 C13 CG 1 0.002 5.680 7.000 1.00 1.00 C
HETATM 14 C14 CG 1 1.228 4.972 7.000 1.00 1.00 C
HETATM 15 C15 CG 1 -1.228 7.810 7.000 1.00 1.00 C
HETATM 16 C16 CG 1 -0.002 7.103 7.000 1.00 1.00 C
HETATM 17 C17 CG 1 4.922 1.419 7.000 1.00 1.00 C
HETATM 18 C18 CG 1 6.148 0.711 7.000 1.00 1.00 C
HETATM 19 C19 CG 1 3.692 3.550 7.000 1.00 1.00 C
HETATM 20 C20 CG 1 4.918 2.842 7.000 1.00 1.00 C
HETATM 21 C21 CG 1 2.462 5.680 7.000 1.00 1.00 C
HETATM 22 C22 CG 1 3.688 4.972 7.000 1.00 1.00 C
HETATM 23 C23 CG 1 1.232 7.810 7.000 1.00 1.00 C
HETATM 24 C24 CG 1 2.458 7.103 7.000 1.00 1.00 C
HETATM 25 C25 CG 1 7.382 1.419 7.000 1.00 1.00 C
HETATM 26 C26 CG 1 8.608 0.711 7.000 1.00 1.00 C
HETATM 27 C27 CG 1 6.152 3.550 7.000 1.00 1.00 C
HETATM 28 C28 CG 1 7.378 2.842 7.000 1.00 1.00 C
HETATM 29 C29 CG 1 4.922 5.680 7.000 1.00 1.00 C
HETATM 30 C30 CG 1 6.148 4.972 7.000 1.00 1.00 C
HETATM 31 C31 CG 1 3.692 7.810 7.000 1.00 1.00 C
HETATM 32 C32 CG 1 4.918 7.103 7.000 1.00 1.00 C
HETATM 33 C26 CG 1 -1.232 0.711 7.000 1.00 1.00 C
HETATM 34 C28 CG 1 -2.462 2.842 7.000 1.00 1.00 C
HETATM 35 C30 CG 1 -3.692 4.972 7.000 1.00 1.00 C
HETATM 36 C32 CG 1 -4.922 7.103 7.000 1.00 1.00 C
HETATM 37 C2 CG 1 -3.692 9.233 7.000 1.00 1.00 C
HETATM 38 C10 CG 1 -1.232 9.233 7.000 1.00 1.00 C
HETATM 39 C18 CG 1 1.228 9.233 7.000 1.00 1.00 C
HETATM 40 C26 CG 1 3.688 9.233 7.000 1.00 1.00 C
CONECT 1 33 2 4
CONECT 2 1 9
CONECT 3 34 4 6
CONECT 4 1 3 11
CONECT 5 35 6 8
CONECT 6 3 5 13
CONECT 7 36 8 37
CONECT 8 5 7 15
CONECT 9 2 10 12
CONECT 10 9 17
CONECT 11 4 12 14
CONECT 12 9 11 19
CONECT 13 6 14 16
CONECT 14 11 13 21
CONECT 15 8 16 38
CONECT 16 13 15 23
CONECT 17 10 18 20
CONECT 18 17 25
CONECT 19 12 20 22
CONECT 20 17 19 27
CONECT 21 14 22 24
CONECT 22 19 21 29
CONECT 23 16 24 39
CONECT 24 21 23 31
CONECT 25 18 26 28
CONECT 26 25
CONECT 27 20 28 30
CONECT 28 25 27
CONECT 29 22 30 32
CONECT 30 27 29
CONECT 31 24 32 40
CONECT 32 29 31
CONECT 33 1
CONECT 34 3
CONECT 35 5
CONECT 36 7
CONECT 37 7
CONECT 38 15
CONECT 39 23
CONECT 40 31
END
Li.pbd file
TITLE GROningen MAchine for Chemical Simulation
MODEL 1
ATOM 1 LI LI 0 0.810 8.000 6.000 1.00 0.00
TER
ENDMDL
SO4.pdb file
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 S SO 1 0.000 0.000 -0.000 0.00 0.00 SO
ATOM 2 O SO 1 -0.831 0.831 0.831 0.00 0.00 O
ATOM 3 O SO 1 0.831 0.831 -0.831 0.00 0.00 O
ATOM 4 O SO 1 -0.831 -0.831 -0.831 0.00 0.00 O
ATOM 5 O SO 1 0.831 -0.831 0.831 0.00 0.00 O
END
kindly provide the needful help and suggestion that might help me proceed further