[gmx-users] Silly question?
Justin A. Lemkul
jalemkul at vt.edu
Thu Dec 23 02:37:44 CET 2010
Quoting Sergio Manzetti <sergio.manzetti at 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 <jalemkul at 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 at gromacs.org
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> >
>
========================================
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
========================================
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