TITLE File : 54a8_polyions.mtb Force field : 54A8 (condensed-phase simulations) Reference : Reif et al. J. Chem. Theory Comput. 2012, in press File content : Molecular topology building blocks (polyatomic ions) Format : GROMOS11 Initial file : MMR, PHH, CO, Vienna/Zuerich, June 2012 Time stamp : PHH, Fri Aug 3 17:26:34 CEST 2012 Remark : ***warning*** this file is an auxiliary mtb file - since Nov 2011, these files no longer contain blocks that were redundant with those of the corresponding main mtb file. As a result, make_top must always be called with inclusion of the main mtb file in addition to possible auxiliary ones. Remark : ******************************************************************************** **** topologies must be built using a make_top version of June 2012 or later *** ******************************************************************************** Reason: make_top must recognize negative IAC in patches, which indicate the closest preceding atom with the indicated atom name (used in COO- and BOO- patches to locate the preceding CA) Remark : The main general changes from the 54A(B)7 force-field version to the 54A(B)8 force-field version involve a reparametrization of - the charged amino-acid sidechains of peptides - the charged peptide termini - the lipid DPPC - the uronate residues Remark : This file is new in 54A8 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, June 2012 - finalized for distribution on www.gromos.net Modifications : [list below changes after June 2012 - with initials, location and date - and update time stamp] END FORCEFIELD 54A8 END MAKETOPVERSION 1.1 END # # Supplementary Material to # "New interaction parameters for charged amino acid side chains in the GROMOS force field" # # # -> GROMOS 54A8 topology building blocks of the ten ions considered # # Institute for Molecular Modeling and Simulation, # University of Natural Resources and Life Sciences, 1190 Vienna, Austria # # # 3O # / # 2H-1C FORM # \ # 4O # # # # 3O # / # 2C-1C ACET # \ # 4O # # # # # 4O # / # 3C-2C-1C PROP # \ # 5O # # # # 1H # | # 3H-2N-5H H4C0 # | # 4H # # # # 1C # | # 3H-2N-5H H3C1 # | # 4H # # # # 1C # | # 3C-2N-5H H2C2 # | # 4H # # # # 1C # | # 3C-2N-5H H1C3 # | # 4C # # # # 1C # | # 3C-2N-5C H0C4 # | # 4C # # # # 3H 4H # \ / # 2N # | # 1C # / \ # 6H-5N 8N-10H GUAN # | | # 7H 9H # # # 2H # | # 1N # / \ # 4H-3C 7C-8H IMID # | | # 6H-5N__9C-10H # # MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK FORM SOL TYPE MOLE NAME formate anion # building block (residue, nucleotide, etc.) # RNME FORM # number of atoms, number of preceding exclusions # NMAT,NLIN 4 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H2 21 1 0.16000 0 3 2 3 4 2 C1 12 12 0.27000 0 2 3 4 3 O1 2 16 -0.7150 0 1 4 4 O2 2 16 -0.7150 1 0 # bonds # NB 3 # IB JB MCB 1 2 3 2 3 6 2 4 6 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 22 1 2 4 22 3 2 4 38 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK ACET SOL TYPE MOLE NAME acetate anion # building block (residue, nucleotide, etc.) # RNME ACET # number of atoms, number of preceding exclusions # NMAT,NLIN 4 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C2 16 5 0.16000 0 3 2 3 4 2 C1 12 12 0.27000 0 2 3 4 3 O1 2 16 -0.7150 0 1 4 4 O2 2 16 -0.7150 1 0 # bonds # NB 3 # IB JB MCB 1 2 27 2 3 6 2 4 6 # bond angles # NBA 3 # IB JB KB MCB 1 2 3 22 1 2 4 22 3 2 4 38 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 2 1 3 4 1 # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK PROP SOL TYPE MOLE NAME propanoate anion # building block (residue, nucleotide, etc.) # RNME PROP # number of atoms, number of preceding exclusions # NMAT,NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C3 16 5 0.0000 1 2 2 3 2 C2 15 4 0.1600 0 3 3 4 5 3 C1 12 12 0.2700 0 2 4 5 4 O1 2 16 -0.7150 0 1 5 5 O2 2 16 -0.7150 1 0 # bonds # NB 4 # IB JB MCB 1 2 27 2 3 27 3 4 6 3 5 6 # bond angles # NBA 4 # IB JB KB MCB 1 2 3 15 2 3 4 22 2 3 5 22 4 3 5 38 # improper dihedrals # NIDA 1 # IB JB KB LB MCB 3 2 4 5 1 # dihedrals # NDA 1 # IB JB KB LB MCB 1 2 3 4 40 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK H4C0 SOL TYPE MOLE NAME ammonium cation # building block (residue, nucleotide, etc.) # RNME H4C0 # number of atoms, number of preceding exclusions # NMAT,NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 H1 21 1 0.25 0 4 2 3 4 5 2 N1 8 14 0.00 0 3 3 4 5 3 H2 21 1 0.25 0 2 4 5 4 H3 21 1 0.25 0 1 5 5 H4 21 1 0.25 1 0 # bonds # NB 4 # IB JB MCB 1 2 2 2 3 2 2 4 2 2 5 2 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 10 1 2 4 10 1 2 5 10 3 2 4 10 3 2 5 10 4 2 5 10 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK H3C1 SOL TYPE MOLE NAME monomethylammonium cation # building block (residue, nucleotide, etc.) # RNME H3C1 # number of atoms, number of preceding exclusions # NMAT,NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 54 5 0.20 0 4 2 3 4 5 2 N1 8 14 0.05 0 3 3 4 5 3 H1 21 1 0.25 0 2 4 5 4 H2 21 1 0.25 0 1 5 5 H3 21 1 0.25 1 0 # bonds # NB 4 # IB JB MCB 1 2 21 2 3 2 2 4 2 2 5 2 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 11 1 2 4 11 1 2 5 11 3 2 4 10 3 2 5 10 4 2 5 10 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK H2C2 SOL TYPE MOLE NAME dimethylammonium cation # building block (residue, nucleotide, etc.) # RNME H2C2 # number of atoms, number of preceding exclusions # NMAT,NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 54 5 0.20 0 4 2 3 4 5 2 N1 8 14 0.10 0 3 3 4 5 3 C2 54 5 0.20 0 2 4 5 4 H1 21 1 0.25 0 1 5 5 H2 21 1 0.25 1 0 # bonds # NB 4 # IB JB MCB 1 2 21 2 3 21 2 4 2 2 5 2 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 13 1 2 4 11 1 2 5 11 3 2 4 11 3 2 5 11 4 2 5 10 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK H1C3 SOL TYPE MOLE NAME trimethylammonium cation # building block (residue, nucleotide, etc.) # RNME H1C3 # number of atoms, number of preceding exclusions # NMAT,NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 54 5 0.20 0 4 2 3 4 5 2 N1 8 14 0.15 0 3 3 4 5 3 C2 54 5 0.20 0 2 4 5 4 C3 54 5 0.20 0 1 5 5 H1 21 1 0.25 1 0 # bonds # NB 4 # IB JB MCB 1 2 21 2 3 21 2 4 21 2 5 2 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 13 1 2 4 13 1 2 5 11 3 2 4 13 3 2 5 11 4 2 5 11 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK H0C4 SOL TYPE MOLE NAME tetramethylammonium cation # building block (residue, nucleotide, etc.) # RNME H0C4 # number of atoms, number of preceding exclusions # NMAT,NLIN 5 0 # preceding exclusions #ATOM MAE MSAE # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 54 5 0.200 0 4 2 3 4 5 2 N1 8 14 0.200 0 3 3 4 5 3 C2 54 5 0.200 0 2 4 5 4 C3 54 5 0.200 0 1 5 5 C4 54 5 0.200 1 0 # bonds # NB 4 # IB JB MCB 1 2 21 2 3 21 2 4 21 2 5 21 # bond angles # NBA 6 # IB JB KB MCB 1 2 3 13 1 2 4 13 1 2 5 13 3 2 4 13 3 2 5 13 4 2 5 13 # improper dihedrals # NIDA 0 # IB JB KB LB MCB # dihedrals # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK GUAN SOL TYPE MOLE NAME guanidinium cation # building block (residue, nucleotide, etc.) # RNME GUAN # number of atoms, number of preceding exclusions # NMAT,NLIN 10 0 # preceding exclusions # atoms #ATOM ANM IACM MASS CGMICGM MAE MSAE 1 C1 12 12 0.0100 0 9 2 3 4 5 6 7 8 9 10 2 NH1 10 14 -0.3600 0 4 3 4 5 8 3 HH11 21 1 0.3450 0 1 4 4 HH12 21 1 0.3450 0 0 5 NH2 10 14 -0.3600 0 3 6 7 8 6 HH21 21 1 0.3450 0 1 7 7 HH22 21 1 0.3450 0 0 8 NH3 10 14 -0.3600 0 2 9 10 9 HH31 21 1 0.3450 0 1 10 10 HH32 21 1 0.3450 1 0 # trailing atoms # bonds # NB 9 # IB JB MCB 1 2 11 1 5 11 1 8 11 2 3 2 2 4 2 5 6 2 5 7 2 8 9 2 8 10 2 # bond angles # NBA 12 # IB JB KB MCB 2 1 5 28 2 1 8 28 5 1 8 28 3 2 4 24 6 5 7 24 9 8 10 24 1 2 3 23 1 2 4 23 1 5 7 23 1 5 6 23 1 8 9 23 1 8 10 23 # improper dihedrals # NIDA 4 # IB JB KB LB MCB 1 2 5 8 1 2 3 4 1 1 5 6 7 1 1 8 9 10 1 1 # dihedrals # NDA 3 # IB JB KB LB MCB 5 1 2 3 14 8 1 5 6 14 2 1 8 9 14 # LJ exceptions # NEX 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 54a8_polyions.mtb BLK IMID SOL TYPE MOLE NAME imidazolium cation # building block (residue, nucleotide, etc.) # RNME IMID # number of atoms, number of preceding exclusions # NMAT, NLIN 10 0 # preceding exclusions # ATOM MAE MSAE # atoms # # ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 N 9 14 -0.03 0 9 2 3 7 4 5 8 9 6 10 2 H 21 1 0.32 0 6 3 7 4 5 8 9 3 C 12 12 0.00 0 7 4 5 6 7 9 8 10 4 H 20 1 0.14 0 4 5 6 7 9 5 N 9 14 -0.03 0 5 6 9 7 10 8 6 H 21 1 0.32 0 3 9 7 10 7 C 12 12 0.00 0 3 8 9 10 8 H 20 1 0.14 0 2 9 10 9 C 12 12 0.00 0 1 10 10 H 20 1 0.14 1 0 # # # bonds # NB 10 # # IB JB MCB 1 2 2 1 3 10 1 7 10 3 4 3 3 5 10 5 6 2 5 9 10 7 8 3 7 9 10 9 10 3 # bond angles # NBA 15 # # IB JB KB MCB 2 1 3 36 2 1 7 36 3 1 7 7 1 3 4 36 1 3 5 7 4 3 5 36 3 5 6 36 3 5 9 7 6 5 9 36 1 7 8 36 1 7 9 7 8 7 9 36 5 9 7 7 5 9 10 36 7 9 10 36 # improper dihedrals # NIDA 10 # IB JB KB LB MCB 3 5 9 7 1 1 3 5 9 1 7 1 3 5 1 3 1 7 9 1 1 7 9 5 1 7 1 8 9 1 1 2 3 7 1 3 1 4 5 1 5 3 6 9 1 9 5 7 10 1 # dihedrals # # NDA 0 # IB JB KB LB MCB # LJ exceptions # NEX 0 #@FREELINE END