[gmx-users] ERROR 1 [file lig.itp, line 575]:: ; Duplicate atom index (19) in virtual_sites3

[Adarsh V. K.]

Dear all,
How to overcome this error ?
( ERROR 1 [file lig.itp, line 575]; Duplicate atom index (19) in
virtual_sites3)

I tried after deleting the line which returned an error message
but still the problem does not get resolved.

Command line:
*gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1*
*The above command returns following 'error message' while using with "
ions.mdp "*
----------------------------------------------------------
NOTE 1 [file ions.mdp]:
ERROR 1 [file lig.itp, line 575]:
Duplicate atom index (19) in virtual_sites3
-----------------------------------------------------------
*I tried after deleting the line 575, but it produces another error at a
later stage*
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o
nvt.tpr
gmx mdrun -deffnm nvt -v

------------------------------------------------------------------------------------
starting mdrun 'XX in water'
50000 steps,    100.0 ps.

Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000442, max 0.021883 (between atoms 5216 and 5218)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   5216   5217   61.7    0.1111   0.1125      0.1111
   5216   5218   36.6    0.1111   0.1135      0.1111

Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 201.336624, max 8789.209961 (between atoms 3384 and 3385)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   3384   3385  128.4    0.1111 976.5923      0.1111
   4542   4543  103.1    0.1111 806.7125      0.1111
   4542   4544   90.0    0.1111   0.4553      0.1111
   5216   5217   90.0    0.1125   0.1590      0.1111
   5216   5218   50.4    0.1135   0.1079      0.1111

step 5: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the time step if appropriate.
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
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