Re: [gmx-users] Huge conformational change of ATP molecules

Hi, Indeed that seems to short. So if one has excluded natural processes, the artificial ones remain the only possible ones... Your process does have to include a custom index group, for example... see http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Tue, Feb

Re: [gmx-users] Huge conformational change of ATP molecules

Hi Mark, Thank you for the suggestions, but I don't think it is because of the PBC artifacts. I do centered my protein and ligand with "-center -pbc mol" option. The protein itself looks fine without any breaking. It's just the ATP that moves out and stays at the outer surface of the protein. I d

Re: [gmx-users] Huge conformational change of ATP molecules

Hi, It sounds like you are observing artefacts from http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Tue, Feb 23, 2016 at 6:18 AM Zheng Ruan wrote: > Hi Gromacs Users, > > I'm running 20ns MD simulation of a protein kinase with ATP bond. I use > amber99sb-i

[gmx-users] Huge conformational change of ATP molecules

Hi Gromacs Users, I'm running 20ns MD simulation of a protein kinase with ATP bond. I use amber99sb-ildn force field with parameters of ATP derived from the database of Richard Bryce. What surprised me is that the ATP molecules displays a huge flexibility and conformational change. First, it slip