Quoting Sergio Manzetti <sergio.manze...@vestforsk.no>: > Thanks Justin: here is the top: >
If this is the entire .top, it's missing several critical sections, and most notably you haven't #included a force field prior to defining your molecule. What you have is an .itp file, not a .top. -Justin > > [ moleculetype ] > ; Name nrexcl > BZP 2 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeB chargeB massB > 1 opls_648 1 BZP C1 1 0 12.0107 ; > qtot 0 > 2 opls_648 1 BZP C2 2 0 12.0107 ; > qtot 0 > 3 opls_648 1 BZP C3 3 0 12.0107 ; > qtot 0 > 4 opls_648 1 BZP C4 4 0 12.0107 ; > qtot 0 > 5 opls_145 1 BZP C5 5 0 12.0107 ; > qtot 0 > 6 opls_146 1 BZP 1H5 5 0 1.0079 > ; qtot 0 > 7 opls_145 1 BZP C6 6 0 12.0107 ; > qtot 0 > 8 opls_146 1 BZP 1H6 6 0 1.0079 > ; qtot 0 > 9 opls_145 1 BZP C7 7 0 12.0107 ; > qtot 0 > 10 opls_146 1 BZP 1H7 7 0 1.0079 > ; qtot 0 > 11 opls_145 1 BZP C8 8 0 12.0107 ; > qtot 0 > 12 opls_146 1 BZP 1H8 8 0 1.0079 > ; qtot 0 > 13 opls_648 1 BZP C9 9 0 12.0107 ; > qtot 0 > 14 opls_145 1 BZP C10 10 0 12.0107 ; > qtot 0 > 15 opls_146 1 BZP 1H10 10 0 1.0079 > ; qtot 0 > 16 opls_648 1 BZP C11 11 0 12.0107 ; > qtot 0 > 17 opls_145 1 BZP C12 12 0 12.0107 ; > qtot 0 > 18 opls_146 1 BZP 1H12 12 0 1.0079 > ; qtot 0 > 19 opls_145 1 BZP C13 13 0 12.0107 ; > qtot 0 > 20 opls_146 1 BZP 1H13 13 0 1.0079 > ; qtot 0 > 21 opls_648 1 BZP C14 14 0 12.0107 ; > qtot 0 > 22 opls_145 1 BZP C15 15 0 12.0107 ; > qtot 0 > 23 opls_146 1 BZP 1H15 15 0 1.0079 > ; qtot 0 > 24 opls_145 1 BZP C16 16 0 12.0107 ; > qtot 0 > 25 opls_146 1 BZP 1H16 16 0 1.0079 > ; qtot 0 > 26 opls_145 1 BZP C17 17 0 12.0107 ; > qtot 0 > 27 opls_146 1 BZP 1H17 17 0 1.0079 > ; qtot 0 > 28 opls_648 1 BZP C18 18 0 12.0107 ; > qtot 0 > 29 opls_145 1 BZP C19 19 0 12.0107 ; > qtot 0 > 30 opls_146 1 BZP 1H19 19 0 1.0079 > ; qtot 0 > 31 opls_145 1 BZP C20 20 0 12.0107 ; > qtot 0 > 32 opls_146 1 BZP 1H20 20 0 1.0079 > ; qtot 0 > > [ bonds ] > ; ai aj funct c0 c1 c2 c3 > 1 2 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 1 21 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 > 1 28 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 > 2 3 1 1.430000e-01 4.000000e+05 1.430000e-01 4.000000e+05 > 2 16 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 > 3 4 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 3 31 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 > 4 5 1 1.420000e-01 4.000000e+05 1.420000e-01 4.000000e+05 > 4 13 1 1.430000e-01 4.000000e+05 1.430000e-01 4.000000e+05 > 5 6 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 5 7 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 > 7 8 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 7 9 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 > 9 10 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 9 11 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 11 12 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 11 13 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 13 14 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 14 15 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 14 16 1 1.390000e-01 4.000000e+05 1.390000e-01 4.000000e+05 > 16 17 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 > 17 18 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 17 19 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 19 20 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 19 21 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 21 22 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 22 23 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 22 24 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 24 25 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 24 26 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 26 27 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 26 28 1 1.410000e-01 4.000000e+05 1.410000e-01 4.000000e+05 > 28 29 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 > 29 30 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > 29 31 1 1.400000e-01 4.000000e+05 1.400000e-01 4.000000e+05 > 31 32 1 1.000000e-01 4.000000e+05 1.000000e-01 4.000000e+05 > > [ exclusions ] > ; i excluded from i > 1 2 21 28 > 2 1 3 16 > 3 2 4 31 > 4 3 5 13 > 5 4 6 7 > 6 5 > 7 5 8 9 > 8 7 > 9 7 10 11 > 10 9 > 11 9 12 13 > 12 11 > 13 4 11 14 > 14 13 15 16 > 15 14 > 16 2 14 17 > 17 16 18 19 > 18 17 > 19 17 20 21 > 20 19 > 21 1 19 22 > 22 21 23 24 > 23 22 > 24 22 25 26 > 25 24 > 26 24 27 28 > 27 26 > 28 1 26 29 > 29 28 30 31 > 30 29 > 31 3 29 32 > 32 31 > > [ angles ] > ; ai aj ak funct c0 c1 c2 > c3 > 2 1 21 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 2 1 28 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 21 1 28 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 1 2 3 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 1 2 16 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > 3 2 16 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 2 3 4 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > 2 3 31 1 1.180000e+02 4.000000e+02 1.180000e+02 > 4.000000e+02 > 4 3 31 1 1.230000e+02 4.000000e+02 1.230000e+02 > 4.000000e+02 > 3 4 5 1 1.220000e+02 4.000000e+02 1.220000e+02 > 4.000000e+02 > 3 4 13 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 5 4 13 1 1.180000e+02 4.000000e+02 1.180000e+02 > 4.000000e+02 > 4 5 6 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 4 5 7 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 6 5 7 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 5 7 8 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 5 7 9 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 8 7 9 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 7 9 10 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 7 9 11 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 10 9 11 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 9 11 12 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 9 11 13 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > 12 11 13 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 4 13 11 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 4 13 14 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 11 13 14 1 1.180000e+02 4.000000e+02 1.180000e+02 > 4.000000e+02 > 13 14 15 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 13 14 16 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 15 14 16 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 2 16 14 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 2 16 17 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 14 16 17 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > 16 17 18 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 16 17 19 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 18 17 19 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 17 19 20 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 17 19 21 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > 20 19 21 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 1 21 19 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 1 21 22 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 19 21 22 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 21 22 23 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 21 22 24 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 23 22 24 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 22 24 25 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 22 24 26 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 25 24 26 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 24 26 27 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 24 26 28 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 27 26 28 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 1 28 26 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 1 28 29 1 1.210000e+02 4.000000e+02 1.210000e+02 > 4.000000e+02 > 26 28 29 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 28 29 30 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 28 29 31 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 30 29 31 1 1.200000e+02 4.000000e+02 1.200000e+02 > 4.000000e+02 > 3 31 29 1 1.220000e+02 4.000000e+02 1.220000e+02 > 4.000000e+02 > 3 31 32 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > 29 31 32 1 1.190000e+02 4.000000e+02 1.190000e+02 > 4.000000e+02 > > [ dihedrals ] > ; ai aj ak al funct c0 c1 > c2 c3 > 1 2 21 28 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 2 1 3 16 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 3 2 4 31 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 4 3 5 13 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 5 4 6 7 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 7 5 8 9 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 9 7 10 11 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 11 9 12 13 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 13 4 11 14 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 14 13 15 16 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 16 2 14 17 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 17 16 18 19 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 19 17 20 21 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 21 1 19 22 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 22 21 23 24 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 24 22 25 26 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 26 24 27 28 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 28 1 26 29 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 29 28 30 31 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > 31 3 29 32 1 1.800000e+02 5.000000e+00 1.800000e+02 > 5.000000e+00 > > > > On Wed, Dec 22, 2010 at 7:36 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > > > > Sergio Manzetti wrote: > > > >> > >> > >> > >> I am trying to grompp a molecule, but get the same error again: > >> > >> Program grompp, VERSION 4.5.1 > >> Source code file: topio.c, line: 654 > >> > >> Fatal error: > >> Syntax error - File bzp.itp, line 1 > >> Last line read: > >> '[ moleculetype ]' > >> Invalid order for directive moleculetype > >> For more information and tips for troubleshooting, please check the > >> GROMACS > >> website at http://www.gromacs.org/Documentation/Errors > >> > >> > >> Can any help? > >> > >> > > Something in your topology is out of order. See Chapter 5 of the manual > > for the proper order. Either you've #included one moleculetype inside > > another, or you've done it before the force field has defined. Either way, > > if you want further assistance, you'll have to post some relevant snapshots > > of your topology. > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > 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. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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