[gmx-users] grompp error

[Justin A. Lemkul]

Eduardo Oliveira wrote:
> Ok, thanks for the advice and sorry for sending the attached file.
> 

No apology necessary; I asked for the file.  I just ask that all discussion 
remain on the list, so that others can contribute and learn from it.

-Justin

> ------------------------------------------------------------------------
> *De:* Justin A. Lemkul <jalemkul at vt.edu>
> *Para:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Enviadas:* Terça-feira, 3 de Abril de 2012 16:51
> *Assunto:* Re: [gmx-users] grompp error
> 
> 
> 
> Eduardo Oliveira wrote:
>  > Thanks!
>  >
> 
> Please keep the discussion on the list.  From your .mdp file:
> 
> tc-grps                  = Protein      SOL
> 
> As I suspected, you're not accounting for ions in any way.  You need to. 
> Usually "Protein Non-protein" works just fine for simple systems.
> 
> -Justin
> 
>  >
>  > ------------------------------------------------------------------------
>  > *De:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *Para:* Eduardo Oliveira <eduardobio at yahoo.com.br 
> <mailto:eduardobio at yahoo.com.br>>; Discussion list for GROMACS users 
> <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>  > *Enviadas:* Terça-feira, 3 de Abril de 2012 15:54
>  > *Assunto:* Re: [gmx-users] grompp error
>  >
>  >
>  >
>  > Eduardo Oliveira wrote:
>  >  > Hi all,
>  >  >
>  >  > After i ran grompp I've the following message:
>  >  >
>  >  > Fatal error:
>  >  > 3 atoms are non part of any of the T-coupling groups
>  >  >
>  >  > It is probably in refference to the 3 CL atoms i've introduced 
> into the system to neutralize my protein charge. Here are the command 
> lines for genion and grompp
>  >  >
>  >  > genion_d  -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq 
> -1 -p arath.top
>  >  >
>  >  > grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr
>  >  >
>  >  > Additional information: I'm running GROMACS 4.5.5
>  >  >
>  >
>  > What are your tc-grps?  Please provide your .mdp file.
>  >
>  > -Justin
>  >
>  > -- ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > MILES-IGERT Trainee
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
>  > ========================================
>  >
>  >
> 
> -- ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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