[gmx-users] (no subject) (Soham Sarkar)
ABEL Stephane
Stephane.ABEL at cea.fr
Fri Apr 5 11:55:39 CEST 2019
Hi
In your itp you have a "?"
?; GENERATED BY LigParGen Server
Remove it and the problem will be solved
PS : next time add a title in you message.
Good luck
-
----------------------------------------------------------------------
Message: 1
Date: Fri, 5 Apr 2019 14:26:00 +0530
From: Soham Sarkar <soham9038 at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] (no subject)
Message-ID:
<CA+fBedfs1GAY1d5K-zVDV9fGmzXFENf-iA-MWeTrUUqbwpmihQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
Dear all,
I am using GROMACS-2018. I want to simulate a system which contain
Tertiary Butyl alcohol (TBA) in it. I am facing problems while executing
the GROMPP command. I have defined this residue in aminoacids.rtp.
The error is like
"NOTE 1 [file ions.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 918407885
WARNING 1 [file tba.itp, line 1]:
Too few gb parameters for type ?
Couldn't find topology match for atomtype ?
Aborted (core dumped)"
I have generated the itp file for TBA from ligpargen.
My itp file is
;
?; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;
[ atomtypes ]
opls_135 C1 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_140 H11 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_140 H12 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_140 H13 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_159 C2 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_135 C3 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_140 H31 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_140 H32 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_140 H33 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_154 O4 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_155 H41 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_135 C5 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_140 H51 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_140 H52 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_140 H53 1.0080 0.000 A 2.50000E-01 1.25520E-01
[ moleculetype ]
; Name nrexcl
TBA 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_135 1 TBA C1 1 -0.304408 12.0110
2 opls_140 1 TBA H11 1 0.098297 1.0080
3 opls_140 1 TBA H12 1 0.086235 1.0080
4 opls_140 1 TBA H13 1 0.111410 1.0080
5 opls_159 1 TBA C2 1 0.247098 12.0110
6 opls_135 1 TBA C3 1 -0.299728 12.0110
7 opls_140 1 TBA H31 1 0.101177 1.0080
8 opls_140 1 TBA H32 1 0.110693 1.0080
9 opls_140 1 TBA H33 1 0.110695 1.0080
10 opls_154 1 TBA O4 1 -0.550587 15.9990
11 opls_155 1 TBA H41 1 0.297574 1.0080
12 opls_135 1 TBA C5 1 -0.304401 12.0110
13 opls_140 1 TBA H51 1 0.098298 1.0080
14 opls_140 1 TBA H52 1 0.086234 1.0080
15 opls_140 1 TBA H53 1 0.111413 1.0080
[ bonds ]
2 1 1 0.1090 284512.000
3 1 1 0.1090 284512.000
4 1 1 0.1090 284512.000
5 1 1 0.1529 224262.400
6 5 1 0.1529 224262.400
7 6 1 0.1090 284512.000
8 6 1 0.1090 284512.000
9 6 1 0.1090 284512.000
10 5 1 0.1410 267776.000
11 10 1 0.0945 462750.400
12 5 1 0.1529 224262.400
13 12 1 0.1090 284512.000
14 12 1 0.1090 284512.000
15 12 1 0.1090 284512.000
[ angles ]
; ai aj ak funct c0 c1
c2 c3
2 1 3 1 107.800 276.144
2 1 4 1 107.800 276.144
2 1 5 1 110.700 313.800
1 5 6 1 112.700 488.273
5 6 7 1 110.700 313.800
5 6 8 1 110.700 313.800
5 6 9 1 110.700 313.800
1 5 10 1 109.500 418.400
5 10 11 1 108.500 460.240
1 5 12 1 112.700 488.273
5 12 13 1 110.700 313.800
5 12 14 1 110.700 313.800
5 12 15 1 110.700 313.800
7 6 9 1 107.800 276.144
6 5 10 1 109.500 418.400
3 1 4 1 107.800 276.144
4 1 5 1 110.700 313.800
3 1 5 1 110.700 313.800
10 5 12 1 109.500 418.400
14 12 15 1 107.800 276.144
13 12 14 1 107.800 276.144
7 6 8 1 107.800 276.144
6 5 12 1 112.700 488.273
13 12 15 1 107.800 276.144
8 6 9 1 107.800 276.144
[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1
c2 c3 c4 c5
[ dihedrals ]
; PROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1
c2 c3 c4 c5
6 5 1 2 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 6 8 3 0.628 1.883 0.000 -2.510 -0.000
0.000
6 5 1 4 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 1 2 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 1 4 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 1 3 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 6 9 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 6 7 3 0.628 1.883 0.000 -2.510 -0.000
0.000
6 5 1 3 3 0.628 1.883 0.000 -2.510 -0.000
0.000
12 5 10 11 3 -0.444 3.833 0.728 -4.117 -0.000
0.000
15 12 5 6 3 0.628 1.883 0.000 -2.510 -0.000
0.000
9 6 5 1 3 0.628 1.883 0.000 -2.510 -0.000
0.000
8 6 5 1 3 0.628 1.883 0.000 -2.510 -0.000
0.000
13 12 5 6 3 0.628 1.883 0.000 -2.510 -0.000
0.000
14 12 5 6 3 0.628 1.883 0.000 -2.510 -0.000
0.000
15 12 5 1 3 0.628 1.883 0.000 -2.510 -0.000
0.000
13 12 5 1 3 0.628 1.883 0.000 -2.510 -0.000
0.000
7 6 5 1 3 0.628 1.883 0.000 -2.510 -0.000
0.000
14 12 5 1 3 0.628 1.883 0.000 -2.510 -0.000
0.000
13 12 5 10 3 0.979 2.937 0.000 -3.916 -0.000
0.000
15 12 5 10 3 0.979 2.937 0.000 -3.916 -0.000
0.000
14 12 5 10 3 0.979 2.937 0.000 -3.916 -0.000
0.000
11 10 5 1 3 -0.444 3.833 0.728 -4.117 -0.000
0.000
11 10 5 6 3 -0.444 3.833 0.728 -4.117 -0.000
0.000
10 5 6 7 3 0.979 2.937 0.000 -3.916 -0.000
0.000
10 5 1 4 3 0.979 2.937 0.000 -3.916 -0.000
0.000
10 5 1 2 3 0.979 2.937 0.000 -3.916 -0.000
0.000
10 5 1 3 3 0.979 2.937 0.000 -3.916 -0.000
0.000
10 5 6 8 3 0.979 2.937 0.000 -3.916 -0.000
0.000
10 5 6 9 3 0.979 2.937 0.000 -3.916 -0.000
0.000
[ pairs ]
2 6 1
1 7 1
3 6 1
1 8 1
4 6 1
1 9 1
2 10 1
1 11 1
3 10 1
4 10 1
2 12 1
1 13 1
3 12 1
1 14 1
4 12 1
1 15 1
7 10 1
6 11 1
8 10 1
9 10 1
7 12 1
6 13 1
8 12 1
6 14 1
9 12 1
6 15 1
11 12 1
10 13 1
10 14 1
10 15 1
Please tell me where the problem is?
Thanks,
Soham
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