[gmx-users] pdb2gmx

Hello all, I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs. It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that

[gmx-users] Aspartate at high pH

__ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief, Kaleidoscope +44 786 131 6686 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] Could not find force field in current directory

-edit.pdb ldh21.pdb residuetypes.dat Could you, please, indicate where the problem may be? Many thanks, Valentina __ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief

Re: [gmx-users] Could not find force field in current directory

Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief, Kaleidoscope +44 786 131 6686 On 23 Jan 2013, at 18:37, Justin Lemkul jalem...@vt.edu wrote: On 1/23/13 1:22 PM, Valentina Erastova wrote: Dear all, I am having a bit of problem

Re: [gmx-users] Could not find force field in current directory

Just a follow up. I have also tried using g_x2top and I am getting the same error. Kind regards, Valentina __ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief, Kaleidoscope +44 786 131 6686 On 23

Re: [gmx-users] Could not find force field in current directory

Awesome. Thank you very much. I will email you a zip. Kind regards, Valentina __ Dr Valentina Erastova Postdoctoral Research Assistant Department of Earth Sciences Durham University Editor-in-Chief, Kaleidoscope +44 786 131 6686 On 23 Jan 2013, at 18:47, Justin

Re: [gmx-users] Could not find force field in current directory

Ooops, thank you very much! Dyslexic people computers are not a good combination! Valentina On 23 Jan 2013, at 19:03, Justin Lemkul wrote: On 1/23/13 1:50 PM, Valentina Erastova wrote: Awesome. Thank you very much. I will email you a zip. I found the problem: atomtypes.atp

Re: [gmx-users] Could not find force field in current directory

forcefield.itp Forcefield doc should have ff description like AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) В письме от 23 января 2013 18:42:43 пользователь Valentina Erastova написал: Thank you for your reply Justin, it is 4.5.5 ( i haven't yet got