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

[Justin Lemkul]

On 3/19/20 1:25 PM, Adarsh V. K. wrote:
> 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
> -----------------------------------------------------------

This comes from our script exploiting a hack allowed in GROMACS 2016 for 
constructing virtual sites. It is invalid in version 2018 and newer, and 
you should get the latest version of the script from 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs, regenerate the 
topology, and use GROMACS version 2020, which supports virtual site 
construction in a manner fully consistent with CHARMM.

-Justin

> *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)
> ------------------------------------------------------------------------------------------

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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