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

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 
and got
) protein_processed.gro
) posre_protein.itp

) protein_newbox.gro

Then, I add glycines to the protein box:
) gmx insert-molecules -ci gly.gro -nmol 10 -f protein_newbox.gro -o 
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,, posre_protein.itp,, so as to proceed my MD 
setting-up? E.g. should I combine them into one itp and one top file, how to do 
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
Gromacs Users mailing list

* Please search the archive at before posting!

* Can't post? Read

* For (un)subscribe requests visit or send a 
mail to

Reply via email to