[gmx-users] Atomtype opls_116 not found when runnning GROMPP

Justin Lemkul jalemkul at vt.edu
Sun Jun 16 01:38:13 CEST 2019



On 6/12/19 1:24 PM, Fernando Nunes wrote:
> Hello,
>
> I am trying to start a minimization in gromacs with a system containing  a
> LC and a IL, and when I try to introduce water in the system and  minimize,
> while running grompp:
>
>    gmx grompp -f em.mdp -c system-solvated.gro -p system-solvated.top -o
> system-solvated-em.tpr
>
>
>
>
>
>
>
>
>
> *And the output of the error is: Program gmx grompp, VERSION 5.1.2Source
> code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c,
> line: 1353Fatal error:Atomtype opls_116 not foundFor more information and
> tips for troubleshooting, please check the GROMACSwebsite at
> http://www.gromacs.org/Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>-------------------------------------------------------*
>
>
> My topology file is based on a forcefield described in this article
> *J. Chem. Theory Comput.*201713126131-6145
>
> This topology file I then made changes in order to have my system described
> in it resulting in the following:
>
> ; Ionic liquid OPLS-VSIL force field
> ; Version 2/2018
> ; Orlando Acevedo
> ; Email: orlando.acevedo at miami.edu
> ; Contributors: B. Doherty, X. Zhong
> ;
> ; B. Doherty, X. Zhong, O. Acevedo, Virtual Site OPLS Force Field for
> Imidazolium-Based Ionic Liquids,
> ;     J. Phys. Chem. B, 2018, 122, 2962-2974.
> ;
> ; Values given below for use in GROMACS 5.0.7 and in comments are
> traditional OPLS-AA units (e.g., angstroms, kcal/mol, degrees)
>
> #define _FF_OPLS
> #define _FF_OPLSAA
>
> [defaults]
> ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1           3        yes        0.5     0.5
>
> ;;;LOAD ATOM TYPES
> #include
> "/media/fnunes/7ee86f80-6e5d-42c0-aa97-eba3efe53337/OPLS/5CB/mir/testebuilders/atomtypes.itp
> #include
> "/home/fnunes/simulacao/IL/0.8*2009IL/ITP/BMIM_atomtypes_scale0.8.itp"
> #include
> "/home/fnunes/simulacao/IL/0.8*2009IL/ITP/DCA_atomtypes_scale0.8.itp"
>
>
> ;;;LOAD MOLECULES *.itp
> #include
> "/media/fnunes/7ee86f80-6e5d-42c0-aa97-eba3efe53337/OPLS/5CB/mir/testebuilders/RY1Q_23BE1B.itp"
> #include "/home/fnunes/simulacao/IL/0.8*2009IL/ITP/BMIM_scale0.8.itp"
> #include "/home/fnunes/simulacao/IL/0.8*2009IL/ITP/DCA_scale0.8.itp"

Presumably none of these custom force field files introduce the atom 
types (and associated parameters) necessary to include the water 
topology on the next line.

-Justin

> #include "oplsaa.ff/spc.itp"
>
>
> [system]
> ; Name
> LC, IL, water system
>
> [molecules]
> LC xxx
> Cation xxx
> Anion xxx
> SOL    4533
>
> --------------------------------------------------
> Thanks in advance for your time reading this
>
> Best Regards
> Fernando Nunes

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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