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