Add Charge

Atoms can be labeled to show charge values.

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.

Charge assignment requires explicit hydrogens, which can be added beforehand with AddH. Structures often have problems such as truncated sidechains that can lead to non-integral net charges. The Dock Prep tool includes options for fixing such problems prior to running AddH and Add Charge. See also: Coulombic Surface Coloring, Add Ions, Write Prmtop, reading charges from files

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.

Standard residues can be assigned parameters from any of the following force fields (details):

• AMBER ff99SB
• AMBER ff99bsc0
• AMBER ff02pol.r1
• AMBER ff03ua
• AMBER ff03.r1

• AM1-BCC - semi-empirical (AM1) with bond charge correction (BCC)
• Gasteiger - faster method based on atom types and connectivity

Command: labelopt info charge
Command: label

OK initiates processing and dismisses the dialog, Apply initiates processing without dismissing the dialog, and Close simply dismisses the dialog. Help opens this manual page in a browser window.

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

If there are any nonstandard residues, a dialog will appear for specifying their net charges. The charge calculation method can be changed at this point, if desired. For the AM1-BCC method only, Tight convergence can be set to true (default false) to specify stricter convergence of the density matrix. Stricter convergence increases calculation time, typically with little effect on the output charge values.

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 Coulombic Surface Coloring or Minimize Structure

  A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz Jr KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. J Am Chem Soc. 1995 May;117(19):5179-97.

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

  Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers. Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE 3rd, Laughton CA, Orozco M. Biophys J. 2007 Jun 1;92(11):3817-29.

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

  Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation. Cieplak P, Caldwell J, Kollman P. J Comput Chem. 2001 Jul 30;22(10):1048-57.
  
  Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. Wang ZX, Zhang W, Wu C, Lei H, Cieplak P, Duan Y. J Comput Chem. 2006 Apr 30;27(6):781-90.

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

  New-generation amber united-atom force field. Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R. J Phys Chem B. 2006 Jul 6;110(26):13166-76.

  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.r1 - charges from all_amino03.lib, all_aminont03.lib, all_aminoct03.lib, all_nucleic94.lib (r1 refers to updated charge sets for N- and C-terminal amino acids; the original ff03 used all_aminont94.lib and all_aminoct94.lib). Original ff03 reference:

  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. J Comput Chem. 2003 Dec;24(16):1999-2012.

• aspartic acid negative or neutral
  • charges for the neutral ASH residue are assigned if one of the carboxylic acid oxygens (preferably OD2 for the proper charge distribution) has atom type O3 and an attached hydrogen
• glutamic acid negative or neutral
  • charges for the neutral GLH residue are assigned if one of the carboxylic acid oxygens (preferably OE2 for the proper charge distribution) has atom type O3 and an attached hydrogen
• cysteine neutral reduced, thiolate (negatively charged), or half-cystine (if there is a disulfide bond)
  • charges for the negative CYM residue are assigned if there is no disulfide bond and no atom named HG
• lysine positive or neutral
  • charges for the neutral LYN residue are assigned if the atom named NZ has atom type N3 and thus two attached hydrogens rather than three
• histidine protonated at δ-nitrogen (neutral), ε-nitrogen (neutral), or both (positive)
  • in AddH, the histidine protonation states can be user-specified or guessed based on the local environment, and in Coulombic Surface Coloring, they can be user-specified; Add Charge recognizes the state from the presence of hydrogen atom HD1, HE2, or both

Comparison of simple potential functions for simulating liquid water. Jorgensen WL, Chandrasekhar J, Madura JD. J Chem Phys. 1983 Jul 15;79(2):926-35.

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.

The available charge calculation methods are:

• 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

Publications involving Antechamber use should cite:

Automatic atom type and bond type perception in molecular mechanical calculations. Wang J, Wang W, Kollman PA, Case DA. J Mol Graph Model. 2006 Oct;25(2):247-60.

Development and testing of a general amber force field. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. J Comput Chem. 2004 Jul 15;25(9):1157-74.

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)

Attribute assignment. Charges can be specified arbitrarily in a simple text attribute assignment file, read in with Define Attribute or the command defattr.

PQR. The PQR variant of PDB format includes atomic partial charges and radii, which Chimera assigns as the atom attributes charge and radius.

Mol2. When a structure is read from a Mol2 file, the Sybyl atom types and any partial charges are stored as the atom attributes mol2type and charge.

PubChem SDF. When a structure is read from a 3D SDF obtained directly from PubChem (see more about these files), values in the section marked <PUBCHEM_MMFF94_PARTIAL_CHARGES> are stored as the atom attribute named charge. Note: SDFs fetched by PubChem CID from within Chimera are from a different database (Pub3D, provided by the CICC at Indiana University) and do not contain charges.

Topology files. Partial charges in some of the topology formats (Amber, PSF) input to MD Movie are stored as the atom attribute named charge.