[gmx-users] genion

[Tamas Horvath]

I've get the following error using grompp

Fatal error: Group Protein_A not found in indexfile.
Maybe you have non-default goups in your mdp file, while not using the '-n'
option of grompp

********
I'm not quite sure what index file it is trying to use, or why is there any
problem...
the corresponding .top file:

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
SOL              5417

***********

Corresponding .mdp file:

tc-grps             =  Protein_A        SOL      Protein_B

*****

here's what I do, before I get to the problem:
pdb2gmx, editconf, genbox
grompp, genion, pdb2gmx
grompp, mdrun (energy min)
grompp (for PosRes) -> throws the error (this is the 1st time where there is
t-coupling)

what am I getting wrong?


On 12/21/05, Tamas Horvath <hotafin at gmail.com> wrote:
>
> Yes, I intended to do so (I mean to create physiological K+, Cl-
> concentrations)
>
> On 12/21/05, Christian Burisch < burisch at bph.rub.de> wrote:
> >
> > Tamas Horvath wrote:
> >
> > Hi all,
> >
> > > Of course I can, but the only way to do that is to capture the pdb2gmx
> > or
> > > grompp output as it seems...
> >
> > it is also in the itp/top-File!
> >
> > grep qtot protein.itp | tail -n 1
> >
> > and then proceed with awk or perl or something like that.
> > Perhaps you should not only neutralise the system, but rather create a
> > physiological ion concentration (which you can calculate of course
> > from the system charge and the number of SOL molecules).
> >
> > HTH
> >
> > Christian
> >
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>
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