[gmx-users] Protein simulation including ligand with Fe(III)

Nikolaos Michelarakis nm884 at york.ac.uk
Tue Aug 5 01:10:05 CEST 2014


I want to run a protein simulation where I will include a ligand which has
an Fe(III) bound on it. So far I have found how to deal with the ligand,
creating its topology seperately and then adding it. Since I am quite new
to MD I have some questions on  how to include the Fe(III) and where.

I have some parameters for the Fe(III) ion. From reading the manual I
understand that I have to go to the forcefield .atp and other files and add
the metal parameters there? Is that correct?

My second question, assuming I have added the parameters successfully, if I
include the ion, which is bound to the ligand, with my protein, run pdb2gmx
and then add the ligand topology separately, will the ion be in the correct
place? It might be a stupid question but I want to make sure. xD

Thank you very much in advance.


More information about the gromacs.org_gmx-users mailing list