[gmx-users] invalid order of directive atomtypes

Justin Lemkul jalemkul at vt.edu
Mon May 9 17:18:19 CEST 2016



On 5/9/16 11:16 AM, Brett wrote:
> Dear All,
>
> Will you please tell me why I got "invalid order of directive atomtypes?
>

Please avail yourself of the very comprehensive Errors page:

http://www.gromacs.org/Documentation/Errors#Invalid_order_for_directive_xxx

-Justin

> Brett
>
> Part of my itp was as following,
>
> ; ADP_BwithH_ADPBfine.itp created by acpype (Rev: 401) on Thu May  5 09:25:01 2016
> [atomtypes]
> ;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
>  o        o           0.00000  0.00000   A     2.95992e-01   8.78640e-01 ; 1.66  0.2100
>  p5       p5          0.00000  0.00000   A     3.74177e-01   8.36800e-01 ; 2.10  0.2000
>  os       os          0.00000  0.00000   A     3.00001e-01   7.11280e-01 ; 1.68  0.1700
>  c3       c3          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
>  oh       oh          0.00000  0.00000   A     3.06647e-01   8.80314e-01 ; 1.72  0.2104
>  na       na          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ; 1.82  0.1700
>  ca       ca          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
>  nc       nc          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ; 1.82  0.1700
>  cd       cd          0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
>  nb       nb          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ; 1.82  0.1700
>  nh       nh          0.00000  0.00000   A     3.25000e-01   7.11280e-01 ; 1.82  0.1700
>  ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000
>  hn       hn          0.00000  0.00000   A     1.06908e-01   6.56888e-02 ; 0.60  0.0157
>  h1       h1          0.00000  0.00000   A     2.47135e-01   6.56888e-02 ; 1.39  0.0157
>  h5       h5          0.00000  0.00000   A     2.42146e-01   6.27600e-02 ; 1.36  0.0150
>  h2       h2          0.00000  0.00000   A     2.29317e-01   6.56888e-02 ; 1.29  0.0157
>
> [ moleculetype ]
> ;name            nrexcl
>  ADPBfine            3
>
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
>      1    o     1   ADP   O2A    1    -0.947401     16.00000 ; qtot -0.947
>      2   p5     1   ADP    PA    2     1.492904     30.97000 ; qtot 0.546
>      3    o     1   ADP   O1A    3    -0.947401     16.00000 ; qtot -0.402
>      4   os     1   ADP   O3A    4    -0.634601     16.00000 ; qtot -1.036
>      5   p5     1   ADP    PB    5     1.367201     30.97000 ; qtot 0.331
>      6    o     1   ADP   O1B    6    -0.955201     16.00000 ; qtot -0.624
>      7    o     1   ADP   O2B    7    -0.955201     16.00000 ; qtot -1.580
>      8    o     1   ADP   O3B    8    -0.955201     16.00000 ; qtot -2.535
>      9   os     1   ADP   O5'    9    -0.657901     16.00000 ; qtot -3.193
>     10   c3     1   ADP   C5'   10     0.055800     12.01000 ; qtot -3.137
>     11   c3     1   ADP   C4'   11     0.106500     12.01000 ; qtot -3.031
>     12   c3     1   ADP   C3'   12     0.202200     12.01000 ; qtot -2.828
>     13   oh     1   ADP   O3'   13    -0.654101     16.00000 ; qtot -3.482
>     14   c3     1   ADP   C2'   14     0.067000     12.01000 ; qtot -3.415
>     15   oh     1   ADP   O2'   15    -0.613901     16.00000 ; qtot -4.029
>     16   c3     1   ADP   C1'   16     0.039400     12.01000 ; qtot -3.990
>     17   os     1   ADP   O4'   17    -0.354800     16.00000 ; qtot -4.345
>
> Par of my topl file was as following,
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
>
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Protein_chain_C.itp"
> #include "topol_Protein_chain_D.itp"
> #include "topol_Protein_chain_E.itp"
> #include "topol_Protein_chain_F.itp"
> #include "topol_Protein_chain_G.itp"
> #include "topol_Protein_chain_H.itp"
> #include "topol_Protein_chain_I.itp"
> #include "topol_Protein_chain_J.itp"
> #include "topol_Protein_chain_K.itp"
> #include "topol_Protein_chain_L.itp"
> #include "topol_Protein_chain_M.itp"
> #include "topol_Protein_chain_N.itp"
>
> ; Include ligand topology
> #include "ADPBfine.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> Protein_chain_C     1
> Protein_chain_D     1
> Protein_chain_E     1
> Protein_chain_F     1
> Protein_chain_G     1
> Protein_chain_H     1
> Protein_chain_I     1
> Protein_chain_J     1
> Protein_chain_K     1
> Protein_chain_L     1
> Protein_chain_M     1
> Protein_chain_N     1
> ADPBfine               1
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================


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