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MCCCS Towhee (Gromos 43A1)

 

 

Overview
    This section covers the Gromos 43A1 force field as it is implemented into the towhee_ff_Gromos43A1 file in the ForceFields directory. All of the Towhee atom, bond angle, and dihedral potential numbers for the Gromos 43A1 force field are listed, along with a short description of their meanings. Unlike almost all of the other force fields implemented into Towhee, Gromos 43A1 cannot be used with the molecule assembler (inpstyle 2) as they have not presented their parameters in a way that facilitates such an assembler, and I have not yet figured out how to create a set of atom types that would work with the assembler. One of the main barriers to such an assembler is that Gromos 43A1 does not apply the same torsional potential to all dihedrals that are connected by the same atom types. Instead Gromos 43A1 applies the torsional potential to only one of the torsions across the same two central atoms of a dihedral, and the rest interact only via 1-4 van der Waals and coulombic terms. For more information about the Gromos force field see the Gromos web site. Note that Gromos 43A1 is a Lennard-Jones (12-6) force field, but it has a rather complex algorithm for computing the cross interactions and so its parameters are listed explicitly (starting with Towhee Version 4.4.0) and so you cannot mix it with any of the other force fields in Towhee. I would like to acknowledge Lukas D. Schuler for providing very useful guidance about implementing Gromos 43A1, and a copy of the relevent pages of the Gromos manual. Any discrepencies (especially typos) from the published Gromos 43A1 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 Gromos 43A1
    The literature reference for Gromos 43A1 is Unfortunately this reference does not actually contain the Gromos 43A1 parameters. In order to get the parameters you need a copy of the Gromos users manual. It appears that the only way to get the users manual is to purchase the Gromos code, but here is the reference for the users manual in case you want to give it a try. A copy of the portions of the users manual related to the force field was generously provided to me by Lukas D. Schuler.
Gromos 43A1 Towhee
    The official force field name for Gromos 43A1 in Towhee is 'Gromos43A1', although that will not get you very far as the molecule assembler does not yet work for Gromos43A1. In order to make the use of Gromos 43A1 as convienent as possible without the use of the molecule builder, I have numbered the atoms, vibrations, bending angles, dihedral angles, and improper torsions using (almost) the same numbering conventions as Gromos 43A1. You will be forced to use inpstyle 0, but hopefully these lists will make the task possible for those who really wish to use Gromos 43A1. The descriptions below include the comments from the Gromos users manual, with any additional comments I felt useful in [square brackets].
    Atom numbers : Gromos atom name : description of the atom
    • 1 : O : carbonyl oxygen (C=0)
    • 2 : OM : carboxyl oxygen (CO)
    • 3 : OA : hydroxyl, sugar or ester oxygen
    • 4 : OW : water oxygen
    • 5 : N : peptide nitrogen (NH)
    • 6 : NT : terminal nitrogen (NH2)
    • 7 : NL : terminal nitrogen (NH3)
    • 8 : NR : aromatic nitrogen
    • 9 : NZ : Arg NH (NH2)
    • 10 : NE : Arg NE (NH)
    • 11 : C : bare carbon
    • 12 : CH1 : aliphatic or sugar CH group
    • 13 : CH2 : aliphatic or sugar CH2 group
    • 14 : CH3 : aliphatic CH3 group
    • 15 : CH4 : methane
    • 16 : CR1 : aromatic CH group
    • 17 : HC : hydrogen bond to carbon [where the carbon is not aliphatic or you would use the appropriate united-atom CHx group]
    • 18 : H : hydrogen not bound to carbon
    • 19 : DUM : dummy atom [not sure what this is for, but implemented it anyway]
    • 20 : S : sulfur
    • 21 : CU1+ : copper (charge 1+)
    • 22 : CU2+ : copper (charge 2+)
    • 23 : FE : iron (heme)
    • 24 : ZN2+ : zinc (charge 2+)
    • 25 : MG2+ : magnesium (charge 2+)
    • 26 : CA2+ : calcium (charge 2+)
    • 27 : P : phosphorous
    • 28 : AR : argon
    • 29 : F : fluorine (non-ionic)
    • 30 : CL : chlorine (non-ionic)
    • 31 : BR : bromine (non-ionic)
    • 32 : CMet : CH3 group in methanol
    • 33 : OMet : oxygen in methanol
    • 34 : NA+ : sodium (charge 1+)
    • 35 : CL- : chlorine (charge 1-)
    • 36 : CChl : carbon in chloroform
    • 37 : CLChl : chlorine in chloroform
    • 38 : HChl : hydrogen in chloroform
    • 39 : SDmso : sulfur in DMSO
    • 40 : CDmso : CH3 group in DMSO
    • 41 : ODmso : oxygen in DMSO
    • 42 : CCl4 : carbon in carbontetrachloride
    • 43 : CLCl4 : chlorine in carbontetrachloride
    • 44 : SI : silicon
    Bond Vibration numbers : Gromos examples of the vibration
    • 1 : H-OA
    • 2 : H-N (all)
    • 3 : HC-C
    • 4 : C-O
    • 5 : C-OM
    • 6 : CR1-NR (6-ring)
    • 7 : H-S
    • 8 : C-NT,NL
    • 9 : C,CR1-N,NR,CR1,C (peptide, 5-ring)
    • 10 : C-N,NA,NE
    • 11 : C-NR (no H)(6-ring)
    • 12 : C-OA
    • 13 : C-NR (heme)
    • 14 : CH2-C,CR1 (6-ring)
    • 15 : C,CR1-CH2,C,CR1 (6-ring)
    • 16 : C,CR1,CH2-NR (6-ring)
    • 17 : CHn-OA
    • 18 : CHn-OM
    • 19 : CHn-OA (sugar)
    • 20 : CHn-N,NT,NL,NZ,NE
    • 21 : CHn-NR (5-ring)
    • 22 : CHn-NR (6-ring)
    • 23 : O,OM-P
    • 24 : O-S
    • 25 : CHn-CHn (sugar)
    • 26 : C,CHn-C,CHn
    • 27 : OA-P
    • 28 : OA-SI
    • 29 : CH3-S
    • 30 : CH2-S
    • 31 : CH1-SI
    • 32 : NR-FE
    • 33 : S-S
    • 34 : NR(heme)-FE
    • 35 : HWat-OWat
    • 36 : HChl-CChl
    • 37 : CChl-CLChl
    • 38 : ODmso-SDmso
    • 39 : SDmso-CDmso
    • 40 : CCl4-CLCl4
    • 41 : HWat-HWat [I believe this is for use with shake, Towhee cannot handle cyclic 3-mers]
    • 42 : HChl-CLChl
    • 43 : CLChl-CLChl
    • 44 : ODmso-CDmso
    • 45 : CDmso-CDmso
    • 46 : HMet-CMet
    • 47 : CLCl4-CLCl4
    Bending Angle numbers : Gromos examples of the bending angle
    • 1 : NR(heme)-FE-NR(heme)
    • 2 : H-S-CH2
    • 3 : CH2-S-CH3
    • 4 : OA-P-OA
    • 5 : CH2-S-S
    • 6 : NR-C-CR1 (5-ring)
    • 7 : CHn-CHn-CHn,NR(6-ring)(sugar)
    • 8 : CHn,OA-CHn-OA,NR(ring)(sugar)
    • 9 : H-NL,NT-H ; CHn-OA-CHn(sugar)
    • 10 : H-NL-C,CHn ; H-NT-CHn
    • 11 : X-OA,SI-X
    • 12 : CHn,C-CHn-C,CHn,OA,OM,N,NE
    • 13 : OM-P-OA
    • 14 : CHn-CHn-C,CHn,OA,NR,NT,NL
    • 15 : CHn-CH2-S
    • 16 : NR(heme)-FE-NR
    • 17 : H-N-CHn
    • 18 : CHn,C-C-OA,N,NT,NL
    • 19 : H-NE-CH2
    • 20 : CH2-N-CH1
    • 21 : CH3-N-C ; CHn-C-OM
    • 22 : H-NT,NZ,NE-C
    • 23 : H-NT,NZ-H
    • 24 : H-N-CH3,H,HC (6-ring) ; H-NT-CHn
    • 25 : P,SI-OA-CHn,P
    • 26 : N-C-CR1 (6-ring, no H)
    • 27 : NZ-C-NZ,NE
    • 28 : OM-P-OM
    • 29 : O-C-CHn,C ; CH3-N-CHn
    • 30 : CH1,CH2-N-C
    • 31 : H-N-C
    • 32 : O-C-OA,N,NT,NL ; C-NE-CH2
    • 33 : FE-NR-CR1(5-ring)
    • 34 : - [no description is listed about this bending angle in Gromos]
    • 35 : H,HC-5-ring [H atoms bonded to an atom which is part of a 5-ring]
    • 36 : X(noH)-5-ring [non-H atoms bonded to an atom which is part of a 5-ring]
    • 37 : OM-C-OM
    • 38 : 5,6 ring connection
    • 39 : SI-OA-SI
    • 40 : HWat-OWat-HWat
    • 41 : HChl-CChl-CLChl
    • 42 : CLChl-CChl-CLChl
    • 43 : CDmso-SDmso-CDmso
    • 44 : CDmso-SDmso-ODmso
    • 45 : HMet-OMet-CMet
    • 46 : CLCl4-CCl4-CLCl4
    Regular Torsion numbers : Gromos examples of the regular torsion
      Note: Gromos 43A1 only applies one torsion involving the cosine series to each pair of central atoms. The remainder of the torsions only interact via van der Waals and coulombic terms. In Towhee this means you need to set all of the other torsions to the Null torsion type of 6. I have put an X for any atom.
    • 1 : X-C-C-X
    • 2 : X-C-OA-X (at ring)
    • 3 : X-C-OA-X (carboxyl)
    • 4 : X-C-N,NT,NE,NZ,NR-X
    • 5 : X-C-CR1-X (6-ring)
    • 6 : X-CH1(sugar)-NR(base)-X Also used as the NULL torsion.
    • 7 : O-CH1-CHn-not O
    • 8 : O-CH1-CHn-O
    • 9 : X-OA-P-X
    • 10 : X-S-S-X
    • 11 : X-OA-P-X
    • 12 : X-CHn-OA(not sugar)-X
    • 13 : X-CH2-S-X
    • 14 : X-C,CHn,SI-NT,NL,OA(sugar)-X
    • 15 : HC-C-S-X
    • 16 : HC-C-C-X
    • 17 : X-CHn,SI-CHn-X
    • 18 : X-NR-FE-X
    • 19 : X-CHn-N,NE-X
    • 20 : X-CHn-C,NR(ring),CR1-X
    • 21 : X-CHn-NT-X
Coulombic interactions
    Gromos 43A1 uses point charges to represent the molecular electrostatic interactions. There is no automated system for assigning these charges. Instead, you need to look through the Gromos manual ( van Gunsteren et al. 1996) and find molecules which are similar to the one you wish to study.
Improper torsions
    Gromos 43A1 exclusively uses the out-of-plane version of the improper torsions. There are only three types of Gromos 43A1 improper torsions, one for enforcing tetrahedral conformations, one for enforcing planarity, and a special one for heme. In the towhee_input file this improper torsion is specified starting from the central atom, and then three atoms bonded to that atom are listed. Starting with version 2.4.5, Towhee uses the same numbering convention as Gromos 43A1. You will need to specify one of the types listed below.
    Towhee Improper Torsion number : description
    • 1 : planar groups
    • 2 : tetrahedral centers
    • 3 : heme iron
Proteins
    Gromos 43A1 is designed for proteins, but I have not yet implemented this force field into the protein builder.
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Send comments to: Marcus G. Martin
Last updated: September 09, 2012