Re: [gmx-users] How to avoid adding ions close to ligand

On 2012-11-26 21:28, Yun Shi wrote: Hi everyone, I am doing conventional MD of a protein-ligand system with a mobile loop as part of the binding site. Presumably, the positive Arg side chain on the mobile loop will eventually move towards the negative carboxylic group on my ligand. But I found

Re: [gmx-users] How to avoid adding ions close to ligand

I did hope the ions will move out eventually. But after my ~70ns of conventional MD (with duplicate MD runs and the protein as a dimer with identical sequence), they were still there in the binding site. So I assume it would be much better to start without any salt ions beside my ligand. Could

Re: [gmx-users] How to avoid adding ions close to ligand

There is nothing stopping you from replacing the ion in your binding pocket with the original water and then replacing another water elsewhere with the ion at the oxygen's coordintes, then running genconf to renumber the gro file. On 2012-11-26 06:25:47PM -0800, Yun Shi wrote: I did hope the