SourceForge.net Logo
MCCCS Towhee (C19eef1)

 

 

Overview
    This section covers the C19eef1 force field (which is a modified version of Charmm19 that includes the EEF1 implicit solvent model) as it is implemented into the towhee_ff_c19eef1 file in the ForceFields directory. All of the Towhee atom types for the C19eef1 force field are listed, along with a short description of their meanings. Note that Charmm19 is a '12-6 plus solvation' classical_potential with 'explicit' classical_mixrule so it cannot currently be combined with any other forcefields. The implicit water solvation is toggled on and off using the isolvtype variable in the towhee_input file. Any discrepencies (especially typos) from the published C19eef1 force field values are the sole responsibility of Marcus G. Martin, and I welcome feedback on how this implementation compares with other programs.

     

References for C19eef1
    The best literature reference for the C19eef1 forcefield parameters is The best literature reference for the C19eef1 solvation parameters is There are parameter (param19_eef1.inp) and topology (toph19_eef1.inp) files which are extremely helpful, but are only available in the Charmm28 distribution.
C19eef1 in Towhee
    The official force field name for C19eef1 in Towhee is 'C19eef1'. Here I list all of the C19eef1 atom names for use in the towhee_input file, along with a brief description. C19eef1 denotes extended-atom for cases where the hydrogens and the heavy element they are bonded to are all lumped into a single interaction site. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here. I include the atom notes from the Neria paper.
    • 'C' : Carbonyl carbon
    • 'CH1E' : Extended aliphatic carbon with one hydrogen -CH- group
    • 'CH2E' : Extended aliphatic carbon with two hydrogens -CH2- group
    • 'CH3E' : Extended methyl terminal -CH3 group
    • 'CM' : Carbon in carbon monoxide
    • 'CR' : 4-bonded carbon in aromatics and Arginine
    • 'CR1E' : Extended aromatic carbon with one hydrogen
    • 'CT' : aliphatic carbon
    • 'Fe' : Iron
    • 'H' : Polar hydrogen
    • 'HC' : Polar hydrogen (in Arg, Lys, and N term)
    • 'HT' : Water hydrogen, modified TIP3P model
    • 'N' : Nitrogen with no hydrogens
    • 'NC2' : Nitrogen bound to two hydrogens (in Arg.)
    • 'NH1' : Nitrogen bound to one hydrogen
    • 'NH2' : Nitrogen bound to two hydrogens
    • 'NH3' : Nitrogen bound to three hydrogens
    • 'NP' : Pyrole nitrogen
    • 'NR' : Nitrogen in an aromatic ring with no hydrogens
    • 'O' : Carbonyl oxygen
    • 'OC' : Carboxyl oxygen
    • 'OH1' : Hydroxyl oxygen
    • 'OH2' : ST2 water oxygen
    • 'OM' : Heme CO/O2 oxygen
    • 'OS' : Ester oxygen
    • 'OT' : Water oxygen, modified TIP3P model
    • 'S' : Sulfur
    • 'SH1E' : Extended sulfur with one hydrogen
Coulombic Interactions
    C19eef1 utilizes point charges on atomic centers to represent the charge distribution on a molecule. As far as I know, there is no automated system for assigning the charges in C19eef1. However, C19eef1 uses a neutral group approach for most moities found in organic molecules. The charge distibution is similiar to that used in Charmm19, except the ionic side chain amino acids are neutralized, and the specifics on how to do this can be found in Lazaridis and Karplus 1999. Otherwise, it is fairly easy to scan through the example molecular charge distributions found in the files available at the MacKerell research web site and determine what charges to apply to the molecule you wish to simulate.
Improper torsions
    Improper torsions are not automatically generated by the Towhee code as the rules for determining where they are applied are not always straight-forward. C19eef1 exclusively uses the out-of-plane version of the improper torsions, and they are typically centered on an sp2 atom in order to enforce planarity with its three neighbors. These torsions are listed in the C19eef1 literature as i-j-k-l where the angle is the dihedral between i-j-k and j-k-l. The bonding pattern is not completely clear to me, but it appears that either i or l is the central atom which is bonded to all three of the other atoms, and none of the other three atoms are bonded to each other. In the towhee_input file the improper torsions is listed starting from the central atom and the three other atoms are listed in the same order as C19eef1. So, if the central atom is i, then the atoms are listed j, k, l. If the central atom is l then the atoms are listed k, j, i. Remember that you can set the improper type to 0 to have the code automatically determine the improper type (so long as inpstyle is 2).
Proteins
    All of the 20 basic amino acids (including the 3 forms of hystidine) are functional for the C19eef1 force field. I have implemented the atom types and charges according to the published Ch19eef1 values. Below is a complete list of the codes for the 20 amino acids, plus some other functional groups that work with the protein builder. C19eef1 does not apply a torsion across all set of atoms connected by 3 bonds in the amino acids. The torsions are explicitly listed for these systems in the polyc19eef1.F routine. I tried to faithfully reproduce all of their energetics, but had to make some accomodations for tryptophan. They have two torsions in tryptophan that span atoms that are not bonded together and I could not implement those into Towhee without a major reworking of configuartional-bias.
    • 'a0' alanine
    • 'c0' cysteine with hydrogen on the sulfur
    • 'd-' aspartic acid deprotonated
    • 'e-' glutamic acid deprotonated
    • 'f0' phenylalanine
    • 'g0' glycine
    • 'h+' histidine both N protonated
    • 'hd' histidine neutral with only Nd protonated
    • 'he' histidine neutral with only Ne protonated
    • 'i0' isoleucine
    • 'k+' lysine protonated
    • 'l0' leucine
    • 'm0' methionine
    • 'n0' asparagine
    • 'p0' proline (no parameters for N-terminal or C-terminal proline)
    • 'q0' glutamine
    • 'r+' arginine protonated
    • 's0' serine
    • 't0' threonine
    • 'v0' valine
    • 'w0' tryptophan
    • 'y0' tyrosine

 

Return to the Towhee Capabilities web page

 


Send comments to: Marcus G. Martin
Last updated: May 18, 2010