Hi! What files do you have in <ffname>.ff directory?
Do you have files ffbonded.itp ffnonbonded.itp 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 reply Justin, > > it is 4.5.5 ( i haven't yet got to instal 4.6 yet) > i tried it on Mac and Linux. > > Shall I attach the files, may be? > > I have earlier written another forcefield and it worked without problems. > > > > > > 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 18:37, 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 with pdb2gmx, when using self written force > >> field. > >> > >> I have created ClayyFF.ff containing: > >> atomtypes.atp ffbonded.itp ffnonbonded.itp forcefield.doc forfecield.itp > >> molecule.rtp > >> > >> also I have residuetypes.dat, stored next to the ClayFF.ff directory. > >> > >> > >> I run: > >> $ pdb2gmx -f ldh21-edit.pdb -o ldh.gro -p ldh.top -ff ClayFF -ignh > >> > >> I get an error: > >> > >> Fatal error: > >> Could not find force field 'ClayFF' in current directory, install tree or > >> GMXDATA path. > >> > >> But the folder ClayFF.ff is in the directory I am running from: > >> > >> > >> $ ls > >> ClayFF.ff ldh21-edit.pdb ldh21.pdb > >> residuetypes.dat > >> > >> > >> Could you, please, indicate where the problem may be? > > > > What version of Gromacs is this? I cannot reproduce the problem with > > 4.5.5 or 4.6. > > > > -Justin -- Best Regards, Alexey 'Alexxy' Shvetsov Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia Department of Molecular and Radiation Biophysics Gentoo Team Ru Gentoo Linux Dev mailto:alexx...@gmail.com mailto:ale...@gentoo.org mailto:ale...@omrb.pnpi.spb.ru
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