I want to simulate a protein-RNA complex in a salt concentration of 150mM. I neutralised the charge of the system by adding 14 Na+ ions and followed that by adding extra salt concentration using the following commands:
gmx grompp -f ions_C.mdp -c fus_solvated.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o ions_solvated.gro -p topol.top -pname NA -nname CL -np 14
gmx genion -s ions.tpr -o ions_solvated_150mM.gro -p topol.top -pname NA -nname CL -conc 0.15
In the next step:
gmx grompp -f minim.mdp -c ions_solvated_150mM.gro -p topol.top -o em.tpr
I am getting the error: number of coordinates in coordinate file (ions_solvated.gro, 25320)
does not match topology (topol.top, 25292)
The difference is of 28 (which is not divisible by 3, so am not sure how to edit the number of SOL from .gro file). Kindly help me in how I can fix it.
Gabor Balogh
Thanks for your reply. In the manual it is mentioned that -conc flag overwrites the -np/-nn flag. That is why i first neutralised the charges and then added salt. Any idea on this?
Thanks Gabor Balogh
. I solved it by using the following command: gmx genion -s ion.tpr -p topol.top -o fus_solv_ion.gro -pname NA -nname CL -conc 0.15 -neutralit added 150 nM of NaCl ions after neutralising the system with 14 sodium ions.
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