[gmx-users] grompp error

[Eduardo Oliveira]

Ok, thanks for the advice and sorry for sending the attached file.



________________________________
 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>
> *Para:* Eduardo Oliveira <eduardobio at yahoo.com.br>; Discussion list for GROMACS users <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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