AMBER Archive (2008)

Subject: AMBER: ligand unit charge is not zero

From: amor san juan (amor_sanjuan_at_yahoo.com)
Date: Thu May 29 2008 - 03:44:58 CDT

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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