[gmx-users] pdb2gmx

2013-06-04 Thread Valentina Erastova
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 i

[gmx-users] Aspartate at high pH

2013-02-13 Thread Valentina Erastova
ina __ 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 h

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

2013-01-23 Thread Valentina Erastova
tp forcefield.doc 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

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

2013-01-23 Thread Valentina Erastova
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.

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

2013-01-23 Thread Valentina Erastova
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

2013-01-23 Thread Valentina Erastova
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

2013-01-23 Thread Valentina Erastova
ntina 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 wrote: > > > On 1/23/13 1:22 PM, Valentina Erastova wrote: >> Dear all, >> >> I am havi

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

2013-01-23 Thread Valentina Erastova
ldh21-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 Edito