Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

Justin A. Lemkul wrote: S and Fe atoms to be 0.25 +/- 0.2 nm apart. If they are much further Edit that: 0.25 nm +/- 0.02 nm. Apparently my math (and/or typing) skills are suspect first thing in the morning :) -Justin -- Justin A. Lemkul Graduat

Re: [gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

[EMAIL PROTECTED] wrote: Hi Justin, Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said the topology file does contain the bonds and I need not have made the modificatins to specbond.dat. But using the original specbond.dat does not prevent the protonation of CYS. I rename

[gmx-users] Re: Loss of bonds in HEME iron after pdb2gmx

Hi Justin, Thanks for your reply. I am using the gmx Gromacs Forcefield. As you said the topology file does contain the bonds and I need not have made the modificatins to specbond.dat. But using the original specbond.dat does not prevent the protonation of CYS. I renamed CYS as CYS2 in the input p