[gmx-users] Ligand and ion topology

Khadija Amine kh.amine1 at gmail.com
Tue Jul 4 11:33:48 CEST 2017

Dear gromacs users,

I have a protein with GNP ligand and acetate ACT ion that I want to

I have prepared topologies for both GNP and ACT with PRODRG program.

My first question is: Where should I exactly include the ACT.itp and
GNP.itp into topol.top file?

My second question is:
I have Copied and pasted the coordinates from my two molecules files onto
the end of the protein.gro file. I have changed the number at the top or
beginning of the file from as it should be to corrected the total number of
atoms in the file.

Should I change the atom number column and renumber the atoms with the new

Is this will affect the position of the ligand and the ions in the protein

Thank you

*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 33339584

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