Re: [gmx-users] -ignh command removes protonation site of interest

On 4/17/19 4:13 PM, Neena Susan Eappen wrote: Hi Justin, I am trying to simulate a peptide in vacuum and it has been shown that carbonyl oxygen is a favorable site of protonation in gas phase, hence I was looking for protonated carbonyl force field parameters. If you're referring to the

Re: [gmx-users] -ignh command removes protonation site of interest

Hi Justin, I am trying to simulate a peptide in vacuum and it has been shown that carbonyl oxygen is a favorable site of protonation in gas phase, hence I was looking for protonated carbonyl force field parameters. Thank you, Neena From: Neena Susan Eappen

[gmx-users] clarity w.r.t pca analysis of protein and ligand complex

Dear all, I am interested in carrying out PCA analysis of protein and ligand complex in order to understand which ligand binds to protein and restricts the relative movement of the chains of receptor during simulation. I have carried out four simulations of 30 ns each - 1) with just the protein