TITLE File : 56a6@CARBO.mtb Force field : 56A6@CARBO (condensed-phase simulations) Reference : Hansen & Hunenberger. J. Comput. Chem. 2011, 32, 998-1032 File content : Molecular topology building blocks (alpha amino acids, nucleic acids, lipids) Format : GROMOS11 Initial file : HALVOR 56A6@CARBO --- PHH, HSH Zuerich, Oct. 2011 Time stamp : PHH, Sat Jul 28 20:53:07 CEST 2012 Remark : ******************************************************************************** **** topologies must be built using a make_top version of June 2012 or later *** ******************************************************************************** Reason: make_top must recognize negative dihedral-angle type codes in patches, which indicate that, if present, an existing dihedral angle with the given type code must be removed (used in HO2C, HO3C, HO4C, HO6C and C1OH patches for carbohydrates to delete existing T2 or T6/T7 dihedrals assuming a OC instead of a OH) Remark : Change from 53A(B)6 involves a reparametrization of the carbohydrates. There are three new atom types (Or, CH0r, CH1r) and the parameters of an existing atom type (CH2r) are slightly altered. Besides the latter (slight) change, the force field can be used with 53A(B)6 for other biomolecules Remark : This file only contains solvents Remark : There is no B force-field version for this set (use 54B7 instead) Remark : Versions beyond 54A(B)7 [including 54C(D)7, 53A(B)6@OXY, 56A(B)6@CARBO] are only available in GROMOS11 format (i.e. all after the release of May 2011) Remark : PHH, Nov 2011 - finalized GROMOS11 files for local usage only (no web distribution yet) Modifications : [list below changes after Nov 2011 - with initials, location and date - and update time stamp] PHH, 09.11.2011: Renamed 56A6_CARBO to 56A6@CARBO (@: force-field variant; _: auxiliary mtb). PHH, 09.11.2011: Reintroduced a FORCEFIELD block in all GROMOS11 files. PHH, 22.11.2011: Finalized the #@BLOCKTYPE comments in mtb files listing file name, residue code (BLK=...), function (SOL,INI,TER,SVT), type (TYPE=APEP,BPEP,DNUC,RNUC, HEXP,HEXU,MOLE), and full name (NAME=...): intended for later use by make_top. PHH, 26.06.2012: Introduced MAKETOPVERSION blocks in all GROMOS11 files PHH, 12.07.2012: Removed all LINKEXCLUSIONS and PHYSICALCONSTANTS blocks from GROMOS11 auxiliary mtb files (now only included in the main mtb file). As a result (and also since MTBUILBLSOLVENT is only to be found there), make_top must always be called with inclusion of the main mtb file (in addition to the possible auxiliary ones). END FORCEFIELD 56A6@CARBO END MAKETOPVERSION 1.1 END PHYSICALCONSTANTS # FPEPSI: 1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) 0.1389354E+03 # HBAR: Planck's constant HBAR = H/(2* PI) 0.6350780E-01 # SPDL: Speed of light (in nm/ps) 2.9979245800E05 # BOLTZ: Boltzmann's constant 8.31441E-03 END LINKEXCLUSIONS #nearest neighbour exclusions when linking #NRNE 2 END MTBUILDBLSOLVENT #@BLOCKTYPE 56a6@CARBO.mtb BLK H2O SVT TYPE MOLE NAME water (SPC model) #solvent name #RNMES H2O #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 5 16 -.82 2 HW1 21 1 .41 3 HW2 21 1 .41 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 56a6@CARBO.mtb BLK H2OE SVT TYPE MOLE NAME water (SPC-E model) #solvent name #RNMES H2OE #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OW 5 16 -.8476 2 HW1 21 1 .4238 3 HW2 21 1 .4238 #constraints #number 3 # IB JB LENGTH 1 2 0.1 1 3 0.1 2 3 0.163299 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 56a6@CARBO.mtb BLK CHCL3 SVT TYPE MOLE NAME chloroform #solvent name #RNMES CHCL3 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CChl 39 12 .179 2 HChl 41 1 .082 3 CLCh1 40 35 -.087 4 CLCh2 40 35 -.087 5 CLCh3 40 35 -.087 #constraints #number 9 # IB JB LENGTH 1 3 0.1758 1 4 0.1758 1 5 0.1758 2 3 0.233839 2 4 0.233839 2 5 0.233839 3 4 0.290283 3 5 0.290283 4 5 0.290283 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 56a6@CARBO.mtb BLK DMSO SVT TYPE MOLE NAME dimethylsulfoxide #solvent name #RNMES DMSO #number of atoms 4 #atoms #ATOM ANM IAC MASS CG 1 SDmso 42 32 .12753 2 ODmso 44 16 -.44753 3 CDms1 43 5 .16 4 CDms2 43 5 .16 #constraints #number 6 # IB JB LENGTH 1 2 0.153 1 3 0.1937991 1 4 0.1937991 2 3 0.2793883 2 4 0.2793883 3 4 0.2911886 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 56a6@CARBO.mtb BLK CH3OH SVT TYPE MOLE NAME methanol #solvent name #RNMES CH3OH #number of atoms 3 #atoms #ATOM ANM IAC MASS CG 1 OMet 36 16 -.674 2 HMet 21 1 .408 3 CMet 35 5 .266 #constraints #number 3 # IB JB LENGTH 1 2 0.1000 1 3 0.1530 2 3 0.2077 #@FREELINE END MTBUILDBLSOLVENT #@BLOCKTYPE 56a6@CARBO.mtb BLK CCL4 SVT TYPE MOLE NAME carbontetrachloride #solvent name #RNMES CCL4 #number of atoms 5 #atoms #ATOM ANM IAC MASS CG 1 CCl4 45 12 .0 2 CLCl1 46 35 .0 3 CLCl2 46 35 .0 4 CLCl3 46 35 .0 5 CLCl4 46 35 .0 #constraints #number 9 # IB JB LENGTH 1 2 0.176 1 3 0.176 1 4 0.176 1 5 0.176 2 3 0.287407 2 4 0.287407 2 5 0.287407 3 4 0.287407 3 5 0.287407 #@FREELINE END