Add Charge

Add Charge assigns atomic partial charges and Amber/GAFF atom types as the attributes charge and gaffType, respectively.

• Values for atoms in standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are taken from Amber.
• Values for atoms in nonstandard residues (any not classified as standard) are determined using Antechamber, which is included with Chimera.

See also: AddH, Dock Prep, Minimize Structure, Add Ions, Write Prmtop

There are several ways to start Add Charge, a tool in the Structure Analysis and Structure Editing categories. Add Charge is also implemented as the command addcharge.

Models to process can be chosen from the list with the left mouse button. Ctrl-click toggles the status of an individual model. To choose a block of models without dragging, click on the first (or last) and then Shift-click on the last (or first) in the desired block.

Charge model indicates the parameters to use for standard residues (details):

• AMBER ff99SB
• AMBER ff99bsc0
• AMBER ff02pol.r1
• AMBER ff03ua
• AMBER ff03
• AMBER ff03.r1 (default)

AddH will be called as needed to add hydrogens. Potentially ambiguous or rare protonation states, especially in binding sites and nonstandard residues, should be verified and corrected before charges are assigned. For example, extra hydrogens could be deleted, or atom types could be edited (before hydrogen addition) with setattr or Build Structure.

If there are any nonstandard residues, a dialog will appear for specifying the net charge of each nonstandard residue and which charge calculation method should be used (details).

If a nucleic acid chain has a 5' terminal phosphate, the user will be asked whether this group should be deleted; otherwise, its atoms will be assigned charges of zero (the charge sets lack parameters for 5' phosphates).

A warning will appear if the name of any atom in a standard residue is not recognized or a model's net charge is not an integer; details will be reported in the Reply Log. Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved. Note that chain-terminal nucleotide residues will normally have non-integral charges, but the 5' and 3' charges sum to an integer.

Atoms in standard residues (water, standard amino acids, standard nucleic acids, and a few common variants and capping groups) are assigned charges and atom types taken from Amber parameter files. Charge model corresponds to force field version (see the Amber documentation for further details):

• AMBER ff99SB - charges from all_amino94.lib, all_aminont94.lib, all_aminoct94.lib, all_nucleic94.lib (charges and atom type assignments are unchanged from the original ff99); used when Add Charge is called from Minimize Structure

  W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, Jr., D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, "A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules" J Am Chem Soc 117:5179 (1995).

• AMBER ff99bsc0 - same charges as ff99SB but uses atom type CI in nucleic acids

  A. Pérez, I. Marchán, D. Svozil, J. Sponer, T.E. Cheatham III, C.A. Laughton, and M. Orozco, "Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers" Biophys J 92:3817 (2007).

• AMBER ff02pol.r1 - charges from all_amino02.lib, all_aminont02.lib, all_aminoct02.lib, all_nucleic02.lib (r1 uses atom type H0 in glycine)

  P. Cieplak, J. Caldwell, and P. Kollman, "Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation" J Comput Chem 22:1048 (2001).
  
  Z.X. Wang, W. Zhang, C. Wu, H. Lei, P. Cieplak, and Y. Duan, "Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides" J Comput Chem 27:781 (2006).

• AMBER ff03ua - charges from uni_amino03.lib, uni_aminont03.lib, uni_aminoct03.lib, all_nucleic94.lib

  L. Yang, C.H. Tan, M.J. Hsieh, J. Wang, Y. Duan, P. Cieplak, J. Caldwell, P.A. Kollman, and R. Luo, "New-generation amber united-atom force field" J Phys Chem B 110:13166 (2006).

  This "united-atom" force field treats amino acid sidechain aliphatic hydrogens as if they were collapsed onto the corresponding carbons. All nucleic acid hydrogens and amino acid backbone, polar, and aromatic hydrogens are still explicit. This option generates warning messages about the unrecognized and thus uncharged aliphatic hydrogens, which can be safely ignored.
  
  
• AMBER ff03 - charges from all_amino03.lib, all_aminont94.lib, all_aminoct94.lib, all_nucleic94.lib

  Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, "A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations" J Comput Chem 24:1999 (2003).

• AMBER ff03.r1 (default) - charges from all_amino03.lib, all_aminont03.lib, all_aminoct03.lib, all_nucleic94.lib (r1 uses updated charge sets for N- and C-terminal amino acids)

• aspartic acid negative or neutral
• glutamic acid negative or neutral
• cysteine neutral reduced, thiolate (negatively charged), or half-cystine (if there is a disulfide bond)
• lysine positive or neutral
• histidine protonated at δ-nitrogen (neutral), ε-nitrogen (neutral), or both (positive)

Water charges correspond to the TIP3P model:

W.L. Jorgensen, J. Chandrasekhar, and J.D. Madura, "Comparison of simple potential functions for simulating liquid water" J Chem Phys 79:926 (1983).

Cases of unrecognized atoms in standard residues and/or incorrect net charges should be examined and resolved. Approaches include:

• editing the input structure file to contain standard atom names that will be recognized
• using Dock Prep to perform various fixes on a structure before charge assignment
• adding missing atoms with Build Structure
• deleting unrecognized atoms that are deemed unnecessary for later calculations
• deciding it is acceptable for the unrecognized atoms to have zero charge
• assigning charges directly with setattr, defattr, or Define Attribute

Charges and GAFF atom types in nonstandard residues (any not classified as standard) are determined using Amber's Antechamber module, which is included with Chimera.

A dialog will appear for specifying the net charge of each nonstandard residue and which charge calculation method should be used:

• AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC), parametrized to reproduce ab initio (HF/6-31G*) electrostatic potentials
• Gasteiger - iterative partial equalization of orbital electronegativity

While both methods are much faster than ab initio calculations, the Gasteiger method is the faster and more approximate of the two. Regardless of which method is chosen, residues that are monatomic ions will simply be assigned their net charges.

Publications involving Antechamber use should cite:

J. Wang, W. Wang, P.A. Kollman, and D.A. Case, "Automatic atom type and bond type perception in molecular mechanical calculations" J Mol Graph Model 25:247 (2006).

J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case, "Development and testing of a general amber force field." J Comput Chem 25:1157 (2004).

Additional sources of charges and other parameters include:

• Amber parameter database (Bryce Group, University of Manchester)
• REDDB (Université de Picardie Jules Verne and Burnham Institute for Medical Research)