When you include many methanes and they all have a slightly nonzero charge,
the total charge of the entire system (unit) is accumulating. You must go
into your meth.lib file and correct the net charge, keeping all
of the hydrogens at the same charge (so either add -1/4 the net charge to
each hydrogen, or minus the net charge to the carbon).
Dave
On Mon, Jun 22, 2020 at 11:57 AM angad sharma <angadsharma54.gmail.com>
wrote:
> i want to generate parameters for methane, but i am facing some problem
>
>
> antechamber -i meth.pdb -fi pdb -o meth.mol2 -fo mol2 -c bcc
> parmchk2 -i meth.mol2 -f mol2 -o meth.frcmod
>
> tleap
> source leaprc.gaff
> unk = loadmol2 meth.mol2
> check unk
> saveoff unk meth.lib
> quit
> till here it is okay for one unit of methane but i put 0.1M methane in the
> a box ,and do the following commands then i face the given error.
>
> tleap
> source leaprc.gaff
> loadamberparams meth.frcmod
> loadoff meth.lib
> a = loadpdb meth.pdb
> check a
> saveamberparm a a.prmtop a.inpcrd
>
>
> then i get this error
> > check a
> Checking 'a'....
> ERROR: The unperturbed charge of the unit: -0.082000 is not integral.
> WARNING: The unperturbed charge of the unit: -0.082000 is not zero.
> Checking parameters for unit 'a'.
> Checking for bond parameters.
> Checking for angle parameters.
> check: Errors: 1 Warning
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Received on Mon Jun 22 2020 - 09:30:04 PDT
