[gmx-users] Ionic liquid simulation problem.

[Justin Lemkul]

On 9/5/17 2:32 PM, Ednilsom Orestes wrote:
> Dear GROMACS Community,
> 
> I am very new with GROMACS I am trying to run a simulation of an ionic
> liquid (1-butyl-3-methyl-imidazolium and hexafluorophosphate) according to
> the following protocol:
> 
> 1. Prepared the respective PDB files and added/modified the OPLS/AA force
> field parameters updating the atomtypes.atp, aminoacid.rtp, ffbonded.itp
> and ffnonbonded.itp files.
> 
> 2. Used *pdb2gmx* command to create the respective .gro files, as well as,
> the posre.itp and topol.top files chossing OPLS/AA option without solvation.
> 
> 3. Used the *insert-molecules* command to create a box filled with one
> specie (cation) and used the *solva**te* command to add the other specie
> (anion) as solvent into the same box.
> 
> 4. Updated, by hand, the generated topol_box.top (pos_box.top) file
> including the topol.top and the posre.itp files of the other specie (anion)
> at the end of it.
> 
> 5. I them tried to used the *grompp* command to minimize the energy of the
> cations+anions box and got the following error:
> 
> Fatal error:
> Syntax error – File forcefield.itp, line 20
> Last line read:
> ‘1                 3            yes           0.5      0.5'
> Found a second defaut directive.
> 
> Does anyone knows whats is wrong with such a protocol?
> 

This means you've got a syntactically invalid force field file, as you're trying 
to set two [defaults] directives (the actual instructions for the force field 
functional form, so there can only be one).

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================