[gmx-users] Ligand and ion topology
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
Ph.D. Biology and Health
Biochemistry & Bioinformatics
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