[gmx-users] How to configure the gro/itp/top files after running "insert-molecules"?

ZHANG Cheng 272699575 at qq.com
Mon Aug 7 13:34:27 CEST 2017

Dear Gromacs,
I am doing a MD for a protein with glycines.

For glycine, I use 
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got 
) gly.gro
) posre_gly.itp
) topol_gly.top

For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh -merge interactive
) gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
and got
) protein_processed.gro
) posre_protein.itp
) topol_protein.top

) protein_newbox.gro

Then, I add glycines to the protein box:
) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o protein_glycine.gro
and got
) protein_glycine.gro, in which the 10 glycines were appended to the protein residues, as if they belong to the same protein molecule (is this normal?)

Can I ask,
1) How can I configure the itp and top files (i.e. posre_gly.itp, topol_gly.top, posre_protein.itp, topol_protein.top), so as to proceed my MD setting-up? E.g. should I combine them into one itp and one top file, how to do that?
2) Then, I will fill the box with water, then add Na+/Cl- ions, then energy minimization. Is this the correct procedure?

Thank you.

Yours sincerely

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