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 <jalem...@vt.edu> wrote: > > > 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 them, or if you send them to me off-list, I will take a look. > > -Justin > >> 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 >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Research Scientist >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
