[gmx-users] Could not find force field in current directory
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. 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? Many thanks, Valentina __ 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://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
Re: [gmx-users] Could not find force field in current directory
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 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.atpffbonded.itpffnonbonded.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.ffldh21-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 listgmx-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 listgmx-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
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 Jan 2013, at 18:37, Justin Lemkul 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.atpffbonded.itpffnonbonded.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.ffldh21-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 listgmx-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 listgmx-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
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 Lemkul 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 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.itpffnonbonded.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 listgmx-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 listgmx-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 listgmx-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
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.atpffbonded.itpffnonbonded.itp forcefield.doc >>>>>> forfecield.itp molecule.rtp >>>>>> > > Your forcefield.itp is spelled wrong. As such, the force field directory is > not properly recognized. Renaming it to forcefield.itp works, up to the > point where your molecule has mismatching atoms, but I'll leave that for you > to sort out. > > -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 listgmx-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 listgmx-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
Re: [gmx-users] Could not find force field in current directory
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 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 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.itpffnonbonded.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-- > gmx-users mailing listgmx-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 listgmx-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] Aspartate at high pH
Hello! I am simulating Aspartate at pH > 10, so it needs to be fully deprotonated (COO-, COO- and NH2). pdb2gmx allows to easily set side chains to be deprotanted, but is there a straightforward way to make NH2, not NH3+? Thank you very much! Kind regards, Valentina __ 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://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] 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 included the angles, BUT wen I convert to the .top I only get bonds, but not angles (see below). Is there something I am missing or does gromacs not assign angles if no bonds are assigned? Thank you! molecule.rtp [ B31 ] ;# ldh21 [ atoms ] ; atomname atomtype charge chargegroup ; charges were taken from paper by Kuang Wu and J R Schmidt; J Phys Chem C (2012) ; and edited to make it fir LDH31 model and produce +1 o1 ohs -1.113 0 h1 ho 0.464 0 o2 ohs -1.113 0 h2 ho 0.464 0 o3 ohs -1.113 0 h3 ho 0.464 0 o4 ohs -1.113 0 h4 ho 0.464 0 mg1 mgo 1.403 0 al1 ao1.983 0 o5 ohs -1.113 0 h5 ho 0.464 0 o6 ohs -1.113 0 h6 ho 0.464 0 o7 ohs -1.113 0 h7 ho 0.464 0 o8 ohs -1.113 0 h8 ho 0.464 0 mg2 mgo 1.403 0 mg3 mgo 1.403 0 [ bonds ] ; atom1 atom2 parametersindex o1 h1 ohs o2 h2 ohs o3 h3 ohs o4 h4 ohs o5 h5 ohs o6 h6 ohs o7 h7 ohs o8 h8 ohs [ angles ] ; aiajak gromos type mg1 o1 h1 moh mg1 o8 h8 moh mg1 o4 h4 moh mg1 o6 h6 moh mg1 o3 h3 moh mg1 o5 h5 moh al1 o3 h3 moh al1 o5 h5 moh al1 o2 h2 moh al1 o7 h7 moh al1 o4 h4 moh al1 o6 h6 moh mg2 o8 h8 moh mg2 o2 h2 moh mg2 o5 h5 moh mg2 o4 h4 moh mg2 o7 h7 moh mg2 o1 h1 moh mg3 o7 h7 moh mg3 o1 h1 moh mg3 o6 h6 moh mg3 o3 h3 moh mg3 o8 h8 moh mg3 o2 h2 moh ldh31.top ; Include forcefield parameters #include "./ClayFF.ff/forcefield.itp" [ moleculetype ] ; Namenrexcl Other 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 B31 rtp B31 q +1.0 1ohs 1B31 o1 1 -1.113 16 ; qtot -1.113 2 ho 1B31 h1 1 0.464 1.008 ; qtot -0.649 3ohs 1B31 o2 1 -1.113 16 ; qtot -1.762 4 ho 1B31 h2 1 0.464 1.008 ; qtot -1.298 5ohs 1B31 o3 1 -1.113 16 ; qtot -2.411 6 ho 1B31 h3 1 0.464 1.008 ; qtot -1.947 7ohs 1B31 o4 1 -1.113 16 ; qtot -3.06 8 ho 1B31 h4 1 0.464 1.008 ; qtot -2.596 9mgo 1B31mg1 1 1.403 24.31 ; qtot -1.193 10 ao 1B31al1 1 1.983 26.98 ; qtot 0.79 11ohs 1B31 o5 1 -1.113 16 ; qtot -0.323 12 ho 1B31 h5 1 0.464 1.008 ; qtot 0.141 13ohs 1B31 o6 1 -1.113 16 ; qtot -0.972 14 ho 1B31 h6 1 0.464 1.008 ; qtot -0.508 15ohs 1B31 o7 1 -1.113 16 ; qtot -1.621 16 ho 1B31 h7 1 0.464 1.008 ; qtot -1.157 17ohs 1B31 o8 1 -1.113 16 ; qtot -2.27 18 ho 1B31 h8 1 0.464 1.008 ; qtot -1.806 19mgo 1B31mg2 1 1.403 24.31 ; qtot -0.403 20mgo 1B31mg3 1 1.403 24.31 ; qtot 1 [ bonds ] ; aiaj functc0c1c2c3 1 2 1ohs 3 4 1ohs 5 6 1ohs 7 8 1ohs 1112 1ohs 1314 1ohs 1516 1ohs 1718 1ohs ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif [ system ] ; Name God Rules Over Mankind, Animals, Cosmos and Such [ molecules ] ; Compound#mols Other 1-- gmx-users mailing listgmx-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
