Hello Jason,
Thanks for these comments. You are right: my question was really about the
gaff-generated charges and not about the other parameters.
The ligand has 39 atoms - maybe this explains the not so small error.
George
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 12 2014 - 06:30:02 PST
