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

[Fernando Nunes]

Thanks for the fast response, I simply included the forcefield that comes
with gromacs after the defaults and commented the defaults from the
forcefield, and it ran without a problem.

Best Regards
Fernando Nunes

Justin Lemkul <jalemkul at vt.edu> escreveu no dia domingo, 16/06/2019 à(s)
00:38:

>
>
> 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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