Duplicate atom index (1) in virtual_sites3 error when running command "gmx grompp -f ions.mdp "

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1

GROMACS version: 2019.6
GROMACS modification: No
Here post your question
I am running the command “gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr”
I am getting the following error
““Fatal error:
There was 1 error in input file(s)””
because of this error
"
ERROR 1 [file inhib1.itp, line 81]:
Duplicate atom index (1) in virtual_sites3
"
in my itp file:
[ virtual_sites3 ]
; Site from funct a d
10 5 1 1 2 0 -0.220

[ exclusions ]
; ai aj
5 10 1
10 1 1
10 2 1
10 6 1
10 7 1
10 3 1
10 4 1

I am using charmm36-feb2021.ff for protein topology and CGenFF version 4.4 for ligand toplogy.unable to understand why still getting this error. kindly guide.
Regards,
Rijja

2

You’re using a very old version of the script, one that exploited a hack in version 2016 that allowed for duplicate atom indices. Use a newer version of the script from the MacKerell lab website and make sure you’re using the latest GROMACS version to make use of a new type of virtual site construction that halogens require in CGenFF.

3

Hi Jalemkul,thank you for your quick reply.

I am using the feb2021 version of both charmm36 and CGenff.I am using py2 script of cgenff_charmm2gmx.py. Should I use py3, is that the issue?
For gromacs I am using the 2019.6 version.

All are latest except gromacs which is also 2019, which I think does not have the hack.

Kindly guide,
Grateful,
Rijja

4

Hello, have you figured out this issue?