[gmx-users] (no subject)

[Justin Lemkul]

On 8/25/19 8:33 AM, Navneet Kumar Singh wrote:
> 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.*

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Please see the information at 
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs which 
specifically addresses this lone pair issue and how to deal with it. 
GROMACS does not easily support the kinds of lone pair/vsite 
construction that CHARMM requires for this kind of interaction.

-Justin

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

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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