[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
simulate.

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
ones?

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

Thank you

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


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