Fix error for file creation

User discussions
1

Hi
Excuse me, how do I fix the following error?
fatal error:
number of coordinates in coordinate file (solve.gro, 15537)
does not match topology (topol.top, 15612)

2

This means that you have mismatching structure file and topology file, that is you modified in some way the .gro file which now has 75 less atoms than the topology you are referring to for compilation.

What was the last thing you did? Added ions? Added water? Did you modify the box in any way? Remember that if you change the box content you have to update the topology accordingly.

3

Please indicate what stage of MD preparation you are performing.

My guess is that you’re encountering an error in the solvation part.

It’s just a minor indentation error. You open the topol.top file and go to the bottom of the file, where the sol 6720 is placed adjacent to the lig 1.
So just put that sol 6720 in the next line, and also check the spacing between sol and 6720

i hope this will rectify your error. :-)

4

Hi
Excuse me
Added ions

5

Hi
Creates a solvent

6

The above problem is fixed but still it doesn’t create the em .gro file.

7

The DNA receptor is alone

8

so did you tried as above ? and are you still facing the same error?

9

NO, Thank you

10

it does not generate em.gro file as such after the solvation step
pls neturalize the system using

gmx grompp -f ions.mdp -c your previous step output.gro -p topol.top -o ions.tpr

gmx genion -s ions.tpr -p topol.top - conc 0.1 -neutral -o neutralized.gro
select: 15 (sol)

now do energy minimization
so you will get the em.gro file which you are expecting