[gmx-users] Invalid directive impropers
Justin Lemkul
jalemkul at vt.edu
Sun May 28 21:52:24 CEST 2017
On 5/28/17 3:40 PM, Saeed Nasiri wrote:
> Dear all
>
> I created the topol.top and itp files for a specific molecules manually,
> but the "grompp" could not read the improper dihedral. I checked th
> tutorials and previous emails, but I did not find about this problem or how
> to defined the improper dihedral.
>
There's no such thing as a [impropers] directive. They're just [dihedrals] with
an appropriate function type. See Table 5.5 in the PDF manual.
-Justin
> Any help will highly appreciated.
> *********************************************************************************************************************
>
> *gmx_mpi grompp -f minim.mdp -c M1M2_solv.gro -p topol.top -o em.tpr*
> :-) GROMACS - gmx grompp, VERSION 5.1.2 (-:
>
> GROMACS is written by:
> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
> Bjelkmar
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> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
> Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
> Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
> and the project leaders:
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>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
> Uppsala University, Stockholm University and
> the Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
> under the terms of the GNU Lesser General Public License
> as published by the Free Software Foundation; either version 2.1
> of the License, or (at your option) any later version.
>
> GROMACS: gmx grompp, VERSION 5.1.2
> Executable: /usr/local/gromacs/bin/gmx_mpi
> Data prefix: /usr/local/gromacs
> Command line:
> gmx_mpi grompp -f minim.mdp -c M1M2_solv.gro -p topol.top -o em.tpr
>
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
>
> NOTE 1 [file minim.mdp]:
> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> that with the Verlet scheme, nstlist has no effect on the accuracy of
> your simulation.
>
> Setting the LD random seed to 3819485409
> Generated 105 of the 105 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 105 of the 105 1-4 parameter combinations
>
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> *ERROR 1 [file M1.itp, line 224]: Invalid directive impropersERROR 2 [file
> M1.itp, line 226]: No default Proper Dih. typesERROR 3 [file M1.itp, line
> 227]: No default Proper Dih. typesERROR 4 [file M1.itp, line 229]: No
> default Proper Dih. typesERROR 5 [file M1.itp, line 231]: No default
> Proper Dih. typesERROR 6 [file M1.itp, line 232]: No default Proper Dih.
> types*
>
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.2
> Source code file:
> /home/home/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line: 1353
>
> Fatal error:
> Atomtype opls_111 not found
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Halting program gmx grompp
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
>
>
> ################topol.top#####################
> #inM2ude "ff_M1.itp"
> #inM2ude "M1.itp"
> #inM2ude "M2.itp"
>
> ; InM2ude water topology
> #inM2ude "oplsaa.ff/tip3p.itp"
>
> [system]
> M1 M2
>
> [molecules]
> M1 1
> M2 1
>
> SOL 858
> SOL 858
> ###################ff_M1.itp###########################
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 3 yes 0.5 0.5
>
> [ atomtypes ]
>
> ; name at.num mass charge ptype V(c6)
> W(c12)
> C1 6 12.011 -0.17 A 3.50 0.27614
> C2 6 12.011 0.01 A 3.50 0.27614
> CE 6 12.011 -0.05 A 3.50 0.27614
> CS 6 12.011 -0.12 A 3.50 0.27614
> CT 6 12.011 -0.18 A 3.50 0.27614
> CR 6 12.011 -0.11 A 3.55 0.29288
> CW 6 12.011 -0.13 A 3.55 0.29288
> HA 1 1.008 0.21 A 2.42 0.12552
> HCR 1 1.008 0.21 A 2.42 0.12552
> HCW 1 1.008 0.21 A 2.42 0.12552
> HC 1 1.008 0.06 A 2.50 0.12552
> H1 1 1.008 0.13 A 2.50 0.12552
> NA 7 14.007 0.15 A 3.25 0.71128
> Cl 17 35.453 -1 A 3.65 0.8300
>
>
> [ bondtypes ]
>
> ; i j func b0(re/nm) kb (kj/mol
> nm^2)
>
> HC CT 6 0.1090 -284500
> HC CS 6 0.1090 -284500
> HC C2 6 0.1090 -284500
> HC C1 6 0.1090 -284500
> H1 C1 6 0.1090 -284500
>
> CT CS 6 0.1529 224200
> CS C2 6 0.1529 224200
> C2 C1 6 0.1529 224200
>
> CR HCR 6 0.1080 -284500
> CW HCW 6 0.1080 -284500
> CR NA 6 0.1315 399200
> CW NA 6 0.1378 357400
> CW CW 6 0.1341 435200
> NA C1 6 0.1466 141000
>
>
> [ angletypes ]
> ; i j k type th/deg ka/kjmol-1
>
> CT CS C2 1 112.7 488.3
> CS C2 C1 1 112.7 488.3
> C2 C1 NA 1 112.7 488.3
>
> CS CT HC 1 110.7 313.8
> CT CS HC 1 110.7 313.8
> C2 CS HC 1 110.7 313.8
> C2 C1 H1 1 110.7 313.8
> C1 C2 HC 1 110.7 313.8
> CS C2 HC 1 110.7 313.8
>
> HC CT HC 1 107.8 276.1
> HC CS HC 1 107.8 276.1
> HC C2 HC 1 107.8 276.1
> H1 C1 H1 1 107.8 276.1
>
> CW NA CR 1 108.0 585.8
> CW NA C1 1 125.6 585.8
> CR NA C1 1 126.4 585.8
> NA CR HCR 1 125.1 292.9
> NA CR NA 1 109.8 585.8
> NA CW CW 1 107.1 585.8
> NA CW HCW 1 122.0 292.9
> CW CW HCW 1 130.9 292.9
> NA C1 H1 1 110.7 313.8
> NA C1 C2 1 112.7 488.3
>
>
> [ dihedraltypes ]
> ; i j k l type v1 v2 v3 v4
>
> HC CT CS HC 5 0.0000 0.0000 1.3305 0.0000
> HC CS C2 HC 5 0.0000 0.0000 1.3305 0.0000
> HC C2 C1 H1 5 0.0000 0.0000 1.3305 0.0000
>
> CT CS C2 HC 5 0.0000 0.0000 1.5313 0.0000
> CS C2 C1 H1 5 0.0000 0.0000 1.5313 0.0000
> C1 C2 CS HC 5 0.0000 0.0000 1.5313 0.0000
> C2 CS CT HC 5 0.0000 0.0000 1.5313
> 0.0000
> CT CS C2 C1 5 7.2800 -0.6569 1.1673
> 0.0000
>
> CW NA CR NA 5 0.0000 19.4600 0.0000
> 0.0000
> CW NA CR HCR 5 0.0000 19.4600 0.0000
> 0.0000
> C1 NA CR NA 5 0.0000 19.4600 0.0000
> 0.0000
> C1 NA CR HCR 5 0.0000 19.4600 0.0000
> 0.0000
> CR NA CW CW 5 0.0000 12.5500 0.0000
> 0.0000
> CR NA CW HCW 5 0.0000 12.5500 0.0000
> 0.0000
> C1 NA CW CW 5 0.0000 12.5500 0.0000
> 0.0000
> C1 NA CW HCW 5 0.0000 12.5500 0.0000
> 0.0000
> NA CW CW NA 5 0.0000 44.9800 0.0000
> 0.0000
> NA CW CW HCW 5 0.0000 44.9800 0.0000
> 0.0000
> HCW CW CW HCW 5 0.0000 44.9800 0.0000
> 0.0000
> CW NA C1 H1 5 0.0000 0.0000 0.5190
> 0.0000
> CR NA C1 H1 5 0.0000 0.0000 0.0000
> 0.0000
> CW NA C1 C2 5 -7.1535 6.1064 0.7939
> 0.0000
> CR NA C1 C2 5 -5.2691 0.0000 0.0000
> 0.0000
> NA C1 C2 CS 5 -7.4797 3.1642 -1.2026
> 0.0000
> NA C1 C2 HC 5 0.0000 0.0000 0.3670
> 0.0000
>
> ; improper
> CR CW NA C1 2 0.0000 8.3700 0.0000 0.0000
> NA NA CR HCW 2 0.0000 9.2000 0.0000 0.0000
> NA CW CW HCW 2 0.0000 9.2000 0.0000 0.0000
>
> ######################M1.itp#######################
> [ moleculetype ]
> M1 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge
> mass
> 1 CW 1 M1 C1 1 -0.13 12.011
> 2 CW 1 M1 C2 2 -0.13 12.011
> 3 CR 1 M1 C3 3 -0.11 12.011
> 4 HCW 1 M1 H4 4 0.21 1.008
> 5 HCW 1 M1 H5 5 0.21 1.008
> 6 HCR 1 M1 H6 6 0.21 1.008
> 7 NA 1 M1 N7 7 0.15 14.007
> 8 NA 1 M1 N8 8 0.15 14.007
> 9 C1 1 M1 C9 9 -0.17 12.011
> 10 H1 1 M1 H10 10 0.13 1.008
> 11 H1 1 M1 H11 11 0.13 1.008
> 12 C2 1 M1 C12 12 0.01 12.011
> 13 HC 1 M1 H13 13 0.06 1.008
> 14 HC 1 M1 H14 14 0.06 1.008
> 15 CS 1 M1 C15 15 -0.12 12.011
> 16 HC 1 M1 H16 16 0.06 1.008
> 17 HC 1 M1 H17 17 0.06 1.008
> 18 CT 1 M1 C18 18 -0.18 12.011
> 19 HC 1 M1 H19 19 0.06 1.008
> 20 HC 1 M1 H20 20 0.06 1.008
> 21 HC 1 M1 H21 21 0.06 1.008
> 22 C1 1 M1 C22 22 -0.17 12.011
> 23 H1 1 M1 H23 23 0.13 1.008
> 24 H1 1 M1 H24 24 0.13 1.008
> 25 H1 1 M1 H25 25 0.13 1.008
>
>
>
> [ bonds ]
>
> ; ai aj funct
> 1 2 6
> 1 4 6
> 1 7 6
>
> 2 5 6
> 2 8 6
>
> 3 6 6
> 3 7 6
> 3 8 6
>
> 7 22 6
>
> 8 9 6
>
> 9 10 6
> 9 11 6
> 9 12 6
>
> 12 13 6
> 12 14 6
> 12 15 6
>
> 15 16 6
> 15 17 6
> 15 18 6
>
> 18 19 6
> 18 20 6
> 18 21 6
>
> 22 23 6
> 22 24 6
> 22 25 6
>
>
> [ angles ]
> ; ai aj ak funct
>
> 1 7 22 1
> 1 7 3 1
> 1 2 5 1
> 1 2 8 1
>
> 2 1 4 1
> 2 1 7 1
> 2 8 3 1
> 2 8 9 1
>
> 3 7 22 1
> 3 8 9 1
>
> 4 1 7 1
>
> 5 2 8 1
>
> 6 3 7 1
> 6 3 8 1
>
> 7 22 23 1
> 7 22 24 1
> 7 22 25 1
> 7 3 8 1
>
> 8 9 10 1
> 8 9 11 1
> 8 9 12 1
>
> 9 12 13 1
> 9 12 14 1
> 9 12 15 1
>
> 10 9 11 1
> 10 9 12 1
>
> 11 9 12 1
>
> 12 15 16 1
> 12 15 17 1
> 12 15 18 1
>
> 13 12 14 1
> 13 12 15 1
>
> 14 12 15 1
>
> 15 18 19 1
> 15 18 20 1
> 15 18 21 1
>
> 16 15 17 1
> 16 15 18 1
>
> 17 15 18 1
>
> 19 18 20 1
> 19 18 21 1
>
> 20 18 21 1
>
> 23 22 24 1
> 23 22 25 1
>
> 24 22 25 1
>
>
> [ dihedrals ]
>
> ; ai aj ak al funct
>
> 1 2 8 3 5
> 1 2 8 9 5
> 1 7 3 6 5
> 1 7 22 23 5
> 1 7 22 24 5
> 1 7 22 25 5
> 1 7 3 6 5
> 1 7 3 8 5
>
> 2 1 7 22 5
> 2 1 7 3 5
> 2 8 3 6 5
> 2 8 3 7 5
> 2 8 9 10 5
> 2 8 9 11 5
> 2 8 9 12 5
>
> 3 7 1 4 5
> 3 7 22 23 5
> 3 7 22 24 5
> 3 7 22 25 5
> 3 8 2 5 5
> 3 8 9 10 5
> 3 8 9 11 5
> 3 8 9 12 5
>
> 4 1 2 5 5
> 4 1 2 8 5
> 4 1 7 22 5
>
> 5 2 1 7 5
> 5 2 8 9 5
>
> 6 3 7 22 5
> 6 3 8 9 5
>
> 7 3 8 9 5
> 7 1 2 8 5
>
> 8 3 7 22 5
> 8 9 12 13 5
> 8 9 12 14 5
> 8 9 12 15 5
>
> 9 12 15 16 5
> 9 12 15 17 5
> 9 12 15 18 5
>
> 10 9 12 13 5
> 10 9 12 14 5
> 10 9 12 15 5
>
> 11 9 12 13 5
> 11 9 12 14 5
> 11 9 12 15 5
>
> 12 15 18 19 5
> 12 15 18 20 5
> 12 15 18 21 5
>
> 13 12 15 16 5
> 13 12 15 17 5
> 13 12 15 18 5
>
> 14 12 15 16 5
> 14 12 15 17 5
> 14 12 15 18 5
>
> 16 15 18 19 5
> 16 15 18 20 5
> 16 15 18 21 5
>
> 17 15 18 19 5
> 17 15 18 20 5
> 17 15 18 21 5
>
>
>
>
>
>
>
>
>
> *[ impropers ]; atom1 atom2 atom3 atom4 q0 cq 3
> 1 7 22 3 8 2 9 7 8
> 3 5 7 1 2 4*
>
--
==================================================
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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