Respected All,
I am going to do the Ligand MD simulation using Justin Lemkul tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/03_solvate.html). After solvating using these commands
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
when i type the following commands for Adding Ions
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
I stuck here with the below error
Fatal error:
number of coordinates in coordinate file (solv.gro, 32803)
does not match topology (topol.top, 32818)
How ca i fix this error?
Hi Abdul,
The 'JZ4' molecule is not present in the solv.gro file but it is mentioned in the topology and the complex.gro file. So the total number of atoms are not matching. You can see there is a mismatch of 15 atoms and your JZ4 has 15 atoms.
So try to incorporate that in the solv.gro file maintaining the correct .gro format and the correct itp file has to be incorporated in the topol.top file. (using #include)
That will eliminate the error.
thanks.
Good to see that you have fixed it.
If you encounter any problem (even if solved ones !) please try to discuss it at Researchgate. This will be helpful for many beginners.
Thank you.
thanks for your help,
can you please help me in the below question
https://www.researchgate.net/post/How_to_Prepare_the_Ligand_B12_coordinate_file_using_PRODRG_server?_tpcectx=profile_highlights
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