GROMACS version: 2020
GROMACS modification: Yes/No
Here post your question
Hello Everyone
I am doing protein-ligand simulation.
My protein contains 4 chains A, B, C and D.
i used gmx pdb2gmx -f protein.pdb -o protein.gro -p topol_protein.top -i posre_protein.itp -ff amber99sb-ildn -water tip3p -ignh to generate:
topol_Protein_chain_A.itp,
posre_Protein_chain_A.itp,
topol_Protein_chain_B.itp,
posre_Protein_chain_B.itp,
topol_Protein_chain_C.itp,
posre_Protein_chain_C.itp,
topol_Protein_chain_D.itp,
posre_Protein_chain_D.itp,
protein.gro
topol.top
Hi,
GROMACS topology are hierarchical, that means the information ([directive]) in topol.top has to follow a predefined order. First forcefield descriptions, molecules description, system description
To avoid to make to the file too long we use include to include the content from other files.
Here you find details of topol.top format https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
For example
first the forcefield #include “amber99sb-ildn.ff/forcefield.itp” : this includes the information for the force field you are using, including bonded and non-bonded parameters
molecule description for each molecule [moleculetype] [atoms] [bonds]… #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp
…
last system description [molecules] that list all the molecules in the order they appear in the structure file.
Please check that your topol.top follows these rules, all the files are included and the order of the directive is correct in the file, if you have manually modified. From your post I could not understand the order of directive in your topol.top
I hope it helps
Alessandra
