You can balance the negative charge of your nucleotide by the addions or
addions2 in tleap.
amor san juan ha scritto:
> Hi,
>
> I use antechamber in tleap to generate the topology and coordinate for a ligand which is a nucleotide (Formula: C12H20N4O14P3). The warning is that the charge is equal to -3.0. Can anyone give an idea how to solve this warning?
>
> --------------------
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -2.999980 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> old PREP-specified impropers:
> total 0 improper torsions applied
> 0 improper torsions in old prep form
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (no restraints)
>
>> edit MGO
>>
> Unit Editor: > charge MGO
> Unit Editor: Total unperturbed charge: -3.0000
> Unit Editor: Total perturbed charge: -3.0000
>
>> quit
>>
> --------------------------
>
>
>
> Thanks,
> Amor A. San Juan
>
>
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Received on Sun Jun 01 2008 - 06:07:27 PDT
