Problem in creating the input of a protein with 2 chains

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1

GROMACS version: 2024.2
GROMACS modification: No
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I’m trying to do a simulation with a protein (2 chains), but I’m having a problem putting in the command.

gmx pdb2gmx -f protein.pdb -the protein.gro

-Using the Charmm36 force field.

Inside the folder, the files “Posre_Protein_chain_A. ITP", ‘Prosre_Protein_chain_b.itp’, ‘Topol_Protein_chain_a.itp’, ‘Topol_Protein_Chain_B.itp’, ‘Protein.gro’ and ‘Topol.Top’ are created, but the most relevant information is not included in the topology file ‘topol.top’, what would be the correct way to work with this protein?

2

What information do you think is missing? Multi-chain proteins are written to a topol.top file that simply #includes the chain topologies.

3

Dear Prof. @jalemkul ,

When I place the command on a protein with just 1 chain, instead of the files “topol_Protein_chain_A.itp” and “posre_Protein_chain_A.itp” being within the initial folder of the simulation, their information is inserted within the Topol.top file, and so following the calculations in a normal way.

But when the simulation is carried out with 2 chains or more, instead of this information being inserted in the Topol.top file, this information is only inside the main folder, I have already tried to insert it manually inside the topol.top file, but the simulation does not occur correctly. The Topol.top file looks like this:

; Created by:
; :-) GROMACS - gmx pdb2gmx, 2024.2-Homebrew (-:
;
; Executable: /usr/local/bin/…/Cellar/gromacs/2024.2/bin/gmx
; Data prefix: /usr/local/bin/…/Cellar/gromacs/2024.2
; Working dir: /Users/victormoreira/Documents/forum
; Command line:
; gmx pdb2gmx -f 4ey6.pdb -o protein.gro
; Force field was read from the standard GROMACS share directory.
;

; Include forcefield parameters
#include “amber03.ff/forcefield.itp”

; Include chain topologies
#include “topol_Protein_chain_A.itp”
#include “topol_Protein_chain_B.itp”

; Include water topology
#include “amber03.ff/tip3p.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 “amber03.ff/ions.itp”

[ system ]
; Name
Protein

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1

Unfortunately the #Include present in Topol.top does not have the desired effect, thank you for any help.

4

Please explain what this means. You’ve shown an entirely normal multi-chain topology. If you’re getting an error, please tell us exactly what the problem is. A single-chain topology will be written directly to topol.top. Multi-chain topologies are written exactly as shown. Position restraints for each chain should have their #include statements within their respective chain topology files.

5

Dear Prof. @jalemkul ,

Using the tutorial available on the Internet (Protein-Ligand Complex), all the initial steps were performed correctly, but when you arrive at the stage of adding ions through the command:

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

The following error month appears:

Program: gmx grompp, version 2024.2-Homebrew
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 706)

Fatal error:
number of coordinates in coordinate file (solv.gro, 453249)
does not match topology (topol.top, 16380)

6

Likely you have forgotten to update the topology in the solvate and genion steps with the -p option.

7

Thank you teacher @jalemkul ,

In the solvate stage the following commands were used:

gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

But the same error remains.

8

Please copy and paste the [molecules] section of topol.top exactly as it appears.