[gmx-users] (no subject) (Soham Sarkar)
Soham Sarkar
soham9038 at gmail.com
Fri Apr 5 12:13:21 CEST 2019
Hello,
The "?" You are talking about is mistakenly written there. The
original itp file has nothing there and is showing the error. The first few
lines are commented out. So why is that problem? Sorry for not giving a
title. If you want, I can share the original itp file here but as per the
rule I can not attach any sort of files here. So now please tell me what
could be the problem?
On Fri, 5 Apr 2019, 3:26 pm ABEL Stephane, <Stephane.ABEL at cea.fr> wrote:
> 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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