[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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