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, 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
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] (no subject)
> Message-ID:
> <
> ca+fbedfs1gay1d5k-zvdv9fgmzxfenf-ia-mwetruuqbwpm...@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_135C112.0110 0.000A3.5E-01 2.76144E-01
> opls_140 H11 1.0080 0.000A2.5E-01 1.25520E-01
> opls_140 H12 1.0080 0.000A2.5E-01 1.25520E-01
> opls_140 H13 1.0080 0.000A2.5E-01 1.25520E-01
> opls_159C212.0110 0.000A3.5E-01 2.76144E-01
> opls_135C312.0110 0.000A3.5E-01 2.76144E-01
> opls_140 H31 1.0080 0.000A2.5E-01 1.25520E-01
> opls_140 H32 1.0080 0.000A2.5E-01 1.25520E-01
> opls_140 H33 1.0080 0.000A2.5E-01 1.25520E-01
> opls_154O415.9990 0.000A3.12000E-01 7.11280E-01
> opls_155 H41 1.0080 0.000A0.0E+00 0.0E+00
> opls_135C512.0110 0.000A3.5E-01 2.76144E-01
> opls_140 H51 1.0080 0.000A2.5E-01 1.25520E-01
> opls_140 H52 1.0080 0.000A2.5E-01 1.25520E-01
> opls_140 H53 1.0080 0.000A2.5E-01 1.25520E-01
>
> [ moleculetype ]
> ; Name nrexcl
> TBA 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> 1 opls_135 1TBAC1 1-0.304408 12.0110
> 2 opls_140 1TBA H11 1 0.098297 1.0080
> 3 opls_140 1TBA H12 1 0.086235 1.0080
> 4 opls_140 1TBA H13 1 0.111410 1.0080
> 5 opls_159 1TBAC2 1 0.247098 12.0110
> 6 opls_135 1TBAC3 1-0.299728 12.0110
> 7 opls_140 1TBA H31 1 0.101177 1.0080
> 8 opls_140 1TBA H32 1 0.110693 1.0080
> 9 opls_140 1TBA H33 1 0.110695 1.0080
> 10 opls_154 1TBAO4 1-0.550587 15.9990
> 11 opls_155 1TBA H41 1 0.297574 1.0080
> 12 opls_135 1TBAC5 1-0.304401 12.0110
> 13 opls_140 1TBA H51 1 0.098298 1.0080
> 14 opls_140 1TBA H52 1 0.086234 1.0080
> 15 opls_140 1TBA 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
>1110 1 0.0945 462750.400
>12 5 1 0.1529 224262.400
>1312 1 0.1090 284512.000
>1412 1 0.1090 284512.000
>1512 1 0.1090 284512.000
>
> [ angles ]
> ; aiajak functc0c1
> c2c3
> 2 1 3 1107.800276.144
> 2 1 4 1107.800276.144
> 2 1 5 1110.700313.800
> 1 5 6 1112.700
