[gmx-users] OPLS-AA and TIP4P errors

[Alan Wilter Sousa da Silva]

Correct name is "Cl" for gromos87 FF or "CL-" opls and gromos96.

Cheers,
Alan


On Wed, 3 Nov 2004, Dallas Warren wrote:

>
> >[ molecules ]
> >; Compound        #mols
> >Protein             1
> >SOL              4045
> >
> >I edited it to:
> >
> >[ molecules ]
> >; Compound        #mols
> >Protein             1
> >SOL              4037
> >CL                     2
>
> Firstly this should be SOL 4043, since you have only removed two water
> molecules to be replaced with the chloride.  The topology file contains
> number of molecules, not number of atoms.
>
> >and ran:
> >#
> >grompp -v -f lbfgsmin.mdp -c pep1sol1.gro -p pep1sol1.top -o pep1sol1.tpr
> >
> >This returned a error of
> >
> >Fatal error: No such moleculetype CL
> >
> >I of course tried Cl,
> >
> >Fatal error: No such moleculetype Cl
>
> What is the atom/molecule name for chloride with the forcefield that you
> are using?
>
> >What am I missing? Do I need to hand edit the rtp file to include
> >definitions for tip4p water? Forgive my ignorance, I'm just branching out
> >from gromos96 and SPC water.
>
> Hope that helps some (note I haven't used OPLS-AA and TIP4P myself, so
> might be off base, but ....)
>
> Catch ya,
>
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
>

-- 
--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Projeto BioPAUA - HP/LNCC
Petrópolis (RJ), Brasil
www.lncc.br/~alan