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MCCCS Towhee (Charmm22)

 

 

Overview
    This section covers the Charmm22 force field as it is implemented into the towhee_ff_Charmm22 file in the ForceFields directory. All of the Towhee atom types for the Charmm22 force field are listed, along with a short description of their meanings. For more information about the Charmm family of force fields see Bernard Brooks's Charmm home page or the MacKerrel web site or the Charmm.org web site.. Note that Charmm22 is a Lennard-Jones (12-6) force field and can only be combined with other Lennard-Jones (12-6) force fields. I would like to acknowledge Alex D. MacKerrel and Tom B. Woolf for providing useful guidance about implementing Charmm22. Any discrepencies (especially typos) from the published Charmm22 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 Charmm22 Charmm22 in Towhee
    The official force field name for Charmm22 in Towhee is 'Charmm22'. Here I list all of the Charmm22 atom names for use in the towhee_input file, along with a brief description taken from the MacKerell et al. 1998 paper supplementary information. I have added some comments where I thought clarification was needed, these are all in [square brackets]. Please note that the capitalization and spacing pattern is important and must be followed exactly as listed here.
    • 'C' : polar C
    • 'CA' : aromatic C
    • 'CT1' : aliphatic sp3 C for CH
    • 'CT2' : aliphatic sp3 C for CH2
    • 'CT3' : aliphatic sp3 C for CH3
    • 'CPH1' : his CG and CD2 carbons
    • 'CPH2' : his CE1 carbon
    • 'CPT' : trp C between rings
    • 'CY' : trp C in pyrrole ring
    • 'CP1' : tetrahedral C (proline CA)
    • 'CP2' : tetrahedral C (proline CB/CG)
    • 'CP3' : tetrahedral C (proline CD)
    • 'CC' : carbonyl C for sidechains asn, asp, gln, glu
    • 'CD' : carbonyl C for none amides, asp, glu, cter
    • 'CPA' : heme alpha-C
    • 'CPB' : heme beta-C
    • 'CPM' : heme meso-C
    • 'CM' : heme CO carbon
    • 'CS' : thiolate carbon
    • 'CE1' : for alkene; RHC=CR
    • 'CE2' : for alkene; H2C=CR
    • 'FE' : heme iron
    • 'H' : polar H
    • 'HC' : N-ter H
    • 'HA' : nonpolar H
    • 'HT' : TIPS3P water hydrogen
    • 'HP' : aromatic H
    • 'HB' : backbone H
    • 'HR1' : his he1, (+) his HG,HD2
    • 'HR2' : (+) his HE1
    • 'HR3' : neutral his HG, HD2
    • 'HS' : thiol hydrogen
    • 'HA1' : for alkene; RHC=CR
    • 'HA2' : for alkene; H2C=CR
    • 'N' : proline N
    • 'NR1' : neutral his protonated ring nitrogen
    • 'NR2' : neutral his unprotonated ring nitrogen
    • 'NR3' : charged his ring nitrogen
    • 'NH1' : peptide nitrogen
    • 'NH2' : amide nitrogen
    • 'NH3' : ammonium nitrogen
    • 'NC2' : guanidinium nitrogen
    • 'NY' : trp N in pyrrole ring
    • 'NP' : proline ring NH2+ (N-terminal)
    • 'NPH' : heme pyrrole N
    • 'O' : carbonyl oxygen
    • 'OB' : carbonyl oxygen in acetic acid
    • 'OC' : carboxylate oxygen
    • 'OH1' : hydroxyl oxygen
    • 'OS' : ester oxygen
    • 'OT' : TIPS3P water oxygen
    • 'OM' : heme CO/O2 oxygen
    • 'S' : sulphur
    • 'SM' : sulfur C-S-S-C type
    • 'SS' : thiolate sulfur
Coulombic Interactions
    Charmm 22 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 Charmm 22. However, Charmm22 uses a neutral group aproach for most moities found in organic molecules. 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. His Charmm Empirical Force Fields web page is especially helpful.
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. Charmm22 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 Charmm22 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 Charmm22. 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 and the thiol and disulfide forms of cysteine) are functional for the Charmm22 force field. I have implemented the atom types and charges according to the published Charmm22 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.
    • 'a0' alanine
    • 'c0' cysteine with hydrogen on the sulfur
    • 'cs' cysteine in a disulfide bond
    • 'cp' cysteine bonded to palmitate (includes the palmitate)
    • '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
    • 'kr' lysine-like retinal
    • 'l0' leucine
    • 'm0' methionine
    • 'n0' asparagine
    • 'p0' proline
    • 'q0' glutamine
    • 'r+' arginine protonated
    • 's0' serine
    • 't0' threonine
    • 'v0' valine
    • 'w0' tryptophan
    • 'y0' tyrosine
    • 'za' acetyl cap on the N-terminus
    • 'ze' ethanolamine cap on the C-terminus
    • 'zf' formaldahyde cap on the N-terminus
    • 'zm' amide cap (NH2) on the C-terminus. Note: differs from official charmm22 by having a 0.31 charge on both terminal H instead of giving one 0.30 and the other 0.32.
    • 'zn' N-methylamide cap on the C-terminus

 

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Send comments to: Marcus G. Martin
Last updated: May 12, 2006