On Wed, 2014-02-12 at 12:42 +0200, George Patargias wrote:
> Hello
>
> I have created the parameters of a ligand with gaff setting the total
> charge to 0 (which is the default). When I load the generated mol2 into
> tleap and I issue
So `gaff' is technically everything in the force field *except* charges.
The charge derivation is done via some other method (if you used the
default in antechamber, that would be am1-bcc). You seem to be
concerned about the charge derivation more than the force field.
>
> charge lig
>
> I get
>
> Total unperturbed charge: -0.003001
>
> Is this a rounding issue or something?
This is not particularly unusual in my experience (perhaps a little
bigger than I'm used to -- is your ligand large?). You can edit the
charges in the mol2 file by hand by adding 0.003001 to one of the
charges there (probably one of the 'larger' charges) to force
neutrality, or you can add 0.003001/N to each of the atoms in the system
where N is the number of atoms in your ligand -- I don't expect either
choice to make much of a difference.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Feb 12 2014 - 05:30:03 PST
