[gmx-users] (no subject)

[Navneet Kumar Singh]

can you please help in solving this error while running MD simulation of
protein-ligand complex using CHARMM36 force field on GROMACS engine.



*Command*

*gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr*


*ERROR*


*ERROR 1 [file unk.itp, line 497]:  Duplicate atom index (23) in
virtual_sites3*


*------------------------------------------------------------------------------------*

*unk.itp file indicated error/ Please find the attached file for more
details.*


















*   19    22    23     1 9   19    22    23    21 9   51    22    23     1
9   51    22    23    21 9[ virtual_sites3 ]; Site   from funct a   d   52
    1    23    23     2     0   -0.164[ exclusions ]; ai  aj    1    52 1
 52    23 1   52    21 1   52    22 1   52    18 1   52    19 1   52    51
1   52    50 1*


*_______________________________________________________________________*

*CGenFF Server was used to prepare the toplogy and other required files for
th <https://cgenff.umaryland.edu/>e small molecules*



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     Thanks & Regards
_______________________________________________________

[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneetcdl at gmail.com  <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>

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