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 <[email protected]>
*Para:* Discussion list for GROMACS users <[email protected]>
*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 <[email protected] <mailto:[email protected]>>
> *Para:* Eduardo Oliveira <[email protected]
<mailto:[email protected]>>; Discussion list for GROMACS users
<[email protected] <mailto:[email protected]>>
> *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
========================================
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