[gmx-users] ' LONEPAIR LP1 ' gives error message in protein - ligand simulation

[Justin Lemkul]

On 4/17/20 12:15 AM, Adarsh V. K. wrote:
> Dear all,
>
> A ligand molecule (lig) contains a Chlorine atom in it. While attempting to
> performing a protein-ligand simulation, the Gromacs returns an error
> message. It is observed that the
> *CGenFF server *
> Generate two additional lines, as shown below, in lig.str file
>
> ATOM LP1    LPH     0.050 ! on Cl1
> LONEPAIR COLI LP1    Cl1    C18    DIST 1.6400 SCAL 0.0
>
> Which later add an additional line in ' lig.gro ' file generated using
>
> python cgenff_charmm2gmx.py LIG lig_fix.mol2 lig.str charmm36-mar2019.ff
> gmx editconf -f lig_ini.pdb -o lig.gro
>
> at the later stages of simulation, the above 'LP1 lines' gives the
> following error message
> -----------------------------------------------------------------------------------------------------
> WARNING 1 [file topol.top, line 60334]:
>    You are using Ewald electrostatics in a system with net charge. This can
>    lead to severe artifacts, such as ions moving into regions with low
>    dielectric, due to the uniform background charge. We suggest to
>    neutralize your system with counter ions, possibly in combination with a
>    physiological salt concentration.
> -------------------------------------------------------------------------------------------------------
> How to over come this problem while performing a simulation with a ligand
> containing halogens like Chlorine?

Do what the warning tells you and add neutralizing counterions.

> 1) Delete Chlorine atom form the ligand molecule after an optimization with
> Avogadro and before uploading to CGenFF Server ?

Deleting atoms from the ligand is not a reasonable solution. It will 
only make your problem worse because it will leave you with an 
unphysical fractional charge.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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