I would like to create a special index group consisting of protein and lipids (POPG/POPE)

User discussions
1

GROMACS version: 2021.2
GROMACS modification: Yes/No
Here post your question

Please help me to section and merge of group, i am new user and little confused which number i have to choose?
Our Bi-layer model comprises of POPG/POPE. (Generted from Membrane builed)

Version- gmx make_ndx, 2021.2
Command used- gmx make_ndx -f em.gro -o index.ndx

  • 0 System : 42590 atoms
  • 1 Protein : 544 atoms
  • 2 Protein-H : 250 atoms
  • 3 C-alpha : 34 atoms
  • 4 Backbone : 102 atoms
  • 5 MainChain : 134 atoms
  • 6 MainChain+Cb : 164 atoms
  • 7 MainChain+H : 166 atoms
  • 8 SideChain : 378 atoms
  • 9 SideChain-H : 116 atoms
  • 10 Prot-Masses : 544 atoms
  • 11 non-Protein : 42046 atoms
  • 12 Other : 42046 atoms
  • 13 DOPG : 3668 atoms
  • 14 POPE : 17500 atoms
  • 15 POT : 41 atoms
  • 16 CLA : 17 atoms
  • 17 TIP3 : 20820 atoms

I was selected 1|13 and index was genrated. When I ran this command (gmx grompp -f NVT.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr ) I got this error.

ERROR 1…

ERROR 125 [file PROA.itp, line 2687]:
No default Position Rest. types

ERROR 126 [file DOPG.itp, line 1229]:
Incorrect number of parameters - found 2, expected 3 or 6 for Position
Rest. (after the function type).

There were 2 notes

Program: gmx grompp, version 2021.2
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2104)

Fatal error:
There were 126 errors in input file(s)

Please help me to fix this problem. Thank you!

2

Hi,
the way you generate index file and define merged groups Protein and DOPG is correct. If you want to add also POPE then it should be: 1|13|14.
But if you read carefully errors, the problem is in PROA.itp or DOPG.itp files where some parameters are missing. Check them.

See ya.

Ondrej