[gmx-users] Invalid directive impropers
Saeed Nasiri
s.t.nasiri at gmail.com
Sun May 28 21:40:24 CEST 2017
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.
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 (-:
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Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
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) 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
*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*
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