[gmx-users] Ligand and ion topology
kh.amine1 at gmail.com
Tue Jul 4 16:28:54 CEST 2017
Can anyone help, please?
Ph.D. Biology and Health
Biochemistry & Bioinformatics
On Tue, Jul 4, 2017 at 12:33 PM, Khadija Amine <kh.amine1 at gmail.com> wrote:
> 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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