Thanks Justin: here is the top:
[ 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 >
-- 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