GROMACS version: 2022.1
GROMACS modification: No
Here post your question:
Hello and thank you for considering this:):
For the below subsection:
Membrane Protein: KALP15 in DPPC
Step Three: Defining the Unit Cell & Adding Solvent
2. Pack the lipids around the protein
I input the below command for an oligomeric heptamer transmembrane protein:
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
and received the following:
Atom index (4410) in position_restraints out of bounds (1-4409).
This probably means that you have inserted topology section
“position_restraints”
in a part belonging to a different molecule than you intended to.
In that case move the “position_restraints” section to the right molecule.
I HAD ADJUSTED MY TOPOL.TOP TO THE BELOW:
;
; File ‘topol.top’ was generated
; By user: joelsubach (501)
; On host: Joels-MacBook-Air.local
; At date: Fri Jun 24 19:42:53 2022
;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2022.1 (-:
;
; Executable: /usr/local/bin/gmx
; Data prefix: /usr/local
; Working dir: /Users/joelsubach/Desktop/Panx1_Membrane_Protein
; Command line:
; gmx pdb2gmx -f GalaxyPanx1_Seq.pdb -o GalaxyPanx1_Seq_processed.gro -ignh -ter -water spc
; Force field was read from the standard GROMACS share directory.
;
; Include forcefield parameters
#include “gromos53a6_lipid.ff/forcefield.itp”
; Include chain topologies
#include “topol_Protein_chain_A.itp”
#ifdef POSRES
#include “posre_Protein_chain_A.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_A.itp”
#endif
#include “topol_Protein_chain_B.itp”
#ifdef POSRES
#include “posre_Protein_chain_B.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_B.itp”
#endif
#include “topol_Protein_chain_C.itp”
#ifdef POSRES
#include “posre_Protein_chain_C.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_C.itp”
#endif
#include “topol_Protein_chain_D.itp”
#ifdef POSRES
#include “posre_Protein_chain_D.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_D.itp”
#endif
#include “topol_Protein_chain_E.itp”
#ifdef POSRES
#include “posre_Protein_chain_E.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_E.itp”
#endif
#include “topol_Protein_chain_F.itp”
#ifdef POSRES
#include “posre_Protein_chain_F.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_F.itp”
#endif
#include “topol_Protein_chain_G.itp”
#ifdef POSRES
#include “posre_Protein_chain_G.itp”
#endif
#ifdef STRONG_POSRES
#include “strong_posre_Protein_chain_G.itp”
#endif
; Include DPPC chain topology
#include “dppc.itp”
; Include water topology
#include “gromos53a6_lipid.ff/spc.itp”
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include “gromos53a6_lipid.ff/ions.itp”
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
Protein_chain_E 1
Protein_chain_F 1
Protein_chain_G 1
DPPC 108
and again input the below command:
Command line:
** gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr**
and am now getting the below error:
ERROR 1 [file strong_posre_Protein_chain_A.itp, line 4414]:
Atom index (4410) in position_restraints out of bounds (1-4409).
This probably means that you have inserted topology section
“position_restraints”
in a part belonging to a different molecule than you intended to.
In that case move the “position_restraints” section to the right molecule.
with my strong_posre_Protein_chain_A.itp exhibiting the following:
4401 1 100000 100000 100000
4402 1 100000 100000 100000
4403 1 100000 100000 100000
4404 1 100000 100000 100000
4405 1 100000 100000 100000
4406 1 100000 100000 100000
4407 1 100000 100000 100000
4408 1 100000 100000 100000
4409 1 100000 100000 100000
4410 1 100000 100000 100000
4411 1 100000 100000 100000
4412 1 100000 100000 100000
4413 1 100000 100000 100000
4414 1 100000 100000 100000
4415 1 100000 100000 100000
4416 1 100000 100000 100000
4417 1 100000 100000 100000
4418 1 100000 100000 100000
4419 1 100000 100000 100000
4420 1 100000 100000 100000
I believe that the error is within the TOPOL.TOP multiple restraint file formatting portion, any help from any members of this forum would be very helpful, thanks:) Joel