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

2013-01-23 Thread Valentina Erastova
Hi Alexey, Justin found my error - ooops - misspelled one of the filenames. Thank you for your reply! Valentina On 23 Jan 2013, at 19:50, Alexey Shvetsov wrote: > Hi! > > What files do you have in .ff directory? > > Do you have files > ffbonded.itp ffnonbonded.itp forcefield.doc forcefi

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

2013-01-23 Thread Alexey Shvetsov
Hi! What files do you have in .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 пользо

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. > > I found the problem: > >> at

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

2013-01-23 Thread Justin Lemkul
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 ffbonded.itpffnonbonded.itp forcefield.doc forfecield.itp molecule.rtp Your forcefield.itp is spelled wrong. As such, the force field directory

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 Lemkul

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

2013-01-23 Thread Justin Lemkul
On 1/23/13 1:42 PM, Valentina Erastova wrote: 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? The mailing list does not accept attachments. If you provide a link to where I can download t

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 Jan

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

2013-01-23 Thread Valentina Erastova
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 Eras

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

2013-01-23 Thread Justin Lemkul
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.itpffnonbonded.itp forcefield.doc forfecield.itp molecule.rtp also I have residuetype

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

2013-01-23 Thread Valentina Erastova
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.itpffnonbonded.itp forcefield.doc forfecield.itp molecule.rtp also I have residuetypes.dat, stored next to the ClayFF.ff directory.