Chitrita Duttaroy wrote:
Hi,
I am a beginner of Gromacs 3.3.3. <http://3.3.3.>
I have done position restrined grompp with -f pr.mdp, -r .gro (water box
having charge -2e), -c .gro and -p .top (produced by genbox). The output
is a .tpr file.
Then to neutralize the solution with Na+ ion I used genion by -s .tpr -o
.gro - pname NA+ -np 2 -g .log.
Then in the .top file in [molecule] portion I have changed #mol of SOL
by reducing it by 2 and added NA+ of 2 mol to match the coordinate with
.gro. And also deleted the .tpr file. Upto this step everything was OK.
In next step again position restrained grompp was done using .gro file
containing 2 Na+ ions. But which showed a Fatal error --
Fatal error:
2 atoms are not part of any of the T-coupling groups.
So .tpr file is not generated. I am not understanding what to do
now..... Please help as early as possible.
I'm guessing those two atoms are the 2 NA+ (most likely). Every element of your
system should be included in a T-coupling group. Your .mdp file probably has
not assigned the NA+ anywhere (merge it with the solvent in a special group:
SOL_NA+).
-Justin
Thanking you,
CHITRITA DUTTA ROY.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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