Re: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups

Kukol, Andreas wrote: Try without -DFLEXIBLE. See this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html Doesn't -DFLEXIBLE only affect water, not the aromatic rings of the protein? Don't the real problems come from running actual MD with -DFLEXBILE? In some

RE: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups

Try without -DFLEXIBLE. See this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html Andreas --- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of NG HUI WEN Sent: 20 September 2010 04:21 To: gmx-users@gromac

Re: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups

NG HUI WEN wrote: Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increas