hotafin at gmail.com
Wed Dec 21 19:55:36 CET 2005
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
the corresponding .top file:
[ molecules ]
; Compound #mols
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
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-
> 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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