[gmx-users] Ligand and ion topology

[Khadija Amine]

Can anyone help, please?



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

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
> 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
>