read rtf card append * Initial topology guesses generated by * CHARMM General Force Field (CGenFF) program version 0.9.
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1 Electronic Supplementary Material (ESI) for RSC Advances. This journal is The Royal Society of Chemistry 2014 * Stream file for dehydro-amino residues * If using these parameters please cite: * Turpin, ER, Mulholland, S, Bonev, BB & Hirst, JD, RSC Adv., 2014, DOI: /c4ra09897h * eleanor.turpin@nottingham.ac.uk SEPTEMBER 2014 ******** * Initial toppar stream file generated by * CHARMM General Force Field (CGenFF) program version beta * For use with CGenFF version 2b7 * read rtf card append * Initial topology guesses generated by * CHARMM General Force Field (CGenFF) program version beta * 36 1 DECL -C DECL +N DEFA FIRS NTER LAST CTER! Dehydroalanine dipetide! Initial guess of parameters created by ParamChem website! ERT Feb 2013 RESI DHAD 0.000!! H4 O3 O9 H1 ATOM C2 CG ! \ H9 H11 / ATOM H4 HGA ! \ / ATOM H5 HGA ! H5---C2--C4--N8--C6--C5--N10--C1---H2 ATOM H6 HGA ! / \! / \ ATOM C4 CG2O ! H6 C7 H3 ATOM O3 OG2D ! / \! H7 H8 ATOM N8 NG2S ! ATOM H9 HGP ! ATOM C6 CG2D1O 0.310! ATOM C7 CG2DC ! ATOM H7 HGA ! ATOM H8 HGA ! ATOM C5 CG2O ! ATOM O9 OG2D ! ATOM N10 NG2S ! ATOM H11 HGP ! ATOM C1 CG ! ATOM H1 HGA ! ATOM H2 HGA ! ATOM H3 HGA ! DOUBLE C6 BOND C6 BOND C5 BOND C5 BOND C4 BOND O3 BOND C2 C7 N8 C6 O9 N8 C4 C4
2 BOND C5 N10 BOND C1 N10 BOND C1 H1 BOND C1 H2 BOND C1 H3 BOND C2 H4 BOND C2 H5 BOND C2 H6 BOND C7 H7 BOND C7 H8 BOND N8 H9 BOND N10 H11 IMPR C4 C2 N8 O3 IMPR C5 C6 N10 O9 IMPR C6 C7 C5 N8! Dehydrobutyrine dipetide! Based on DHAD residue! ERT Aug 2013 RESI DHBD 0.000!! H4 O3 O9 H1 ATOM C2 CG ! \ H9 H11 / ATOM H4 HGA ! \ / ATOM H5 HGA ! H5---C2--C4--N8--C6--C5--N10--C1---H2 ATOM H6 HGA ! / \! / \ ATOM C4 CG2O ! H6 C7 H8 H3 ATOM O3 OG2D ! / \! H7 C11-H12 ATOM N8 NG2S ! ATOM H9 HGP ! H13 ATOM C6 CG2D1O 0.310! ATOM C7 CG2DC ! ATOM H7 HGA ! ATOM C11 CG ! ATOM H8 HGA ! ATOM H12 HGA ! ATOM H13 HGA ! ATOM C5 CG2O ! ATOM O9 OG2D ! ATOM N10 NG2S ! ATOM H11 HGP ! ATOM C1 CG ! ATOM H1 HGA ! ATOM H2 HGA ! ATOM H3 HGA ! DOUBLE C6 BOND C6 BOND C5 BOND C5 BOND C4 BOND O3 BOND C2 BOND C5 C7 N8 C6 O9 N8 C4 C4 N10
3 BOND C1 N10 BOND C1 H1 BOND C1 H2 BOND C1 H3 BOND C2 H4 BOND C2 H5 BOND C2 H6 BOND C7 H7 BOND N8 H9 BOND N10 H11 BOND C7 C11 BOND C11 H8 BOND C11 H12 BOND C11 H13 IMPR C4 C2 N8 O3 IMPR C5 C6 N10 O9 IMPR C6 C7 C5 N8! Dehydroalanine residue RESI DHAR 0.000!! O! HN!! -N--CA--C--!!! CB! / \! HB1 HB2 ATOM N NG2S ! ATOM HN HGP ! ATOM CA CG2D1O 0.310! ATOM CB CG2DC ! ATOM HB1 HGA ! ATOM HB2 HGA ! ATOM C CG2O ! ATOM O OG2D ! DOUBLE CA CB BOND CA N BOND CA C BOND C O BOND C +N BOND N HN BOND CB HB1 CB HB2 IMPR CA CB C N IMPR C CA +N O DONOR HN N ACCEPTOR O C! Dehydrobutyrine residue! Based on DHAD residue! ERT Aug 2013 RESI DHBR 0.000!! O
4 ! H!! -N--CA--C-!!! CB HG1! / \! HB CG-HG2!! HG3!! ATOM N NG2S ! ATOM HN HGP ! ATOM CA CG2D1O 0.310! ATOM CB CG2DC ! ATOM HB HGA ! ATOM CG CG ! ATOM HG1 HGA ! ATOM HG2 HGA ! ATOM HG3 HGA ! ATOM C CG2O ! ATOM O OG2D ! BOND N HN N CA CA CB CA C C O C +N BOND CB HB CB CG CG HG1 CG HG2 CG HG3 IMPR C CA +N O IMPR CA CB C N DONOR HN N ACCEPTOR O C! alpha-aminobutyric acid, needed for nisin! built by analogy RESI ABU 0.00!! HG1 ATOM N NH1-0.47! ATOM HN H 0.31! HN-N CG-HG2 ATOM CA CT1 0.07! / \ ATOM HA HB1 0.09! / HG3! HA-CA--CB ATOM CB CT2-0.18! / \ ATOM HB1 HA2 0.09! HB1 HB2 ATOM HB2 HA2 0.09! O=C! ATOM CG CT3-0.27! ATOM HG1 HA3 0.09! ATOM HG2 HA3 0.09! ATOM HG3 HA3 0.09!! ATOM C C 0.51! ATOM O O -0.51! BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 BOND CB CG CG HG1 CG HG2 CG HG2 CG HG3 DOUBLE O C
5 IMPR N -C CA HN C CA +N O CMAP -C N CA C N CA C +N DONOR HN N ACCEPTOR O C!Pacth to change charge on C+ PRES DHCC 0.00 ATOM C C ATOM O O !Patch to connect thioether rings, where first res is ALA PRES THIA 0.00 DELETE ATOM 1HB1 DELETE ATOM 2HG1 ATOM 1CB CT ATOM 1HB2 HA ATOM 1HB3 HA ATOM 2SG S ATOM 2CB CT ATOM 2HB1 HA ATOM 2HB2 HA BOND 1CB 2SG!Patch to connect thioether rings, where first res is ABU PRES THIB 0.00 DELETE ATOM 1HB1 DELETE ATOM 2HG1 ATOM 1CB CT ATOM 1HB2 HA ATOM 2SG S ATOM 2CB CT ATOM 2HB1 HA ATOM 2HB2 HA BOND 1CB 2SG END read param card flex append * Initial parameter guess generated by analogy by * CHARMM General Force Field (CGenFF) program version beta * BONDS CG2D1O CG2DC ! Molecule, from CG2D2O CG2DC2, CG2D1O CG2O ! Molecule, from CG2DC1 CG2O1, CG2D1O NG2S ! edited by ERT CG2D1O CG2DC ! Molecule, from CG2D2O CG2DC2, C NG2S ! joining protein & cgenff sets CG2O1 NH ! joining protein & cgenff sets ANGLES CG2DC3 CG2D1O CG2O ! Molecule, from CG2DC3 CG2DC1 CG2O4, CG2DC3 CG2D1O NG2S ! Molecule, from CG2D2 CG2D1O NG321, CG2O1 CG2D1O NG2S ! ERT CG2D1O CG2DC3 HGA ! Molecule, from CG2DC1 CG2DC3 HGA5, CG2D1O CG2O1 NG2S ! Molecule, from CG2DC1 CG2O1 NG2S1,
6 CG2D1O CG2O1 OG2D ! Molecule, from CG2DC1 CG2O1 OG2D1, CG2D1O NG2S1 CG2O ! Molecule, from CG2O1 NG2S1 CG2R61, CG2D1O NG2S1 HGP ! Molecule, from CG2R61 NG2S1 HGP1, CG2DC1 CG2D1O NG2S ! Molecule, from CG2D2 CG2D1O NG321, CG2DC1 CG2D1O CG2O ! Molecule, from CG2DC3 CG2DC1 CG2O4, CG2D1O CG2DC1 CG ! ERT from CG2D1O CG2DC1 CG321! For linking protein and CGenFF parameter sets; analogy w/ prot set CT1 C NG2S O C NG2S C NG2S1 HGP C NG2S1 CG2D1O CG2D1O CG2O1 NH OG2D1 CG2O1 NH CG2O1 NH1 H CG2O1 NH1 CT CG2O1 NH1 CTD CT2 S CT ! from MET CT3 S CT2 DIHEDRALS CG2O1 CG2D1O CG2DC3 HGA ! Molecule, from CG2O4 CG2DC1 CG2DC3 HGA5, NG2S1 CG2D1O CG2DC3 HGA ! Molecule, from CG2DC2 CG2DC1 CG2DC3 HGA5, CG2DC3 CG2D1O NG2S1 HGP ! Molecule, from CG2DC1 CG2O1 NG2S1 HGP1, CG2O1 CG2D1O NG2S1 HGP ! Molecule, from CG2R61 CG2O1 NG2S1 HGP1, CG2D1O CG2O1 NG2S1 HGP ! Molecule, from CG2DC1 CG2O1 NG2S1 HGP1, CG2DC1 CG2D1O NG2S1 CG2O CG2DC1 CG2D1O NG2S1 CG2O CG2DC1 CG2D1O NG2S1 CG2O NG2S1 CG2D1O CG2DC1 HGA !dhb NG2S1 CG2D1O CG2DC1 CG !dhb c11c7c6n8 NG2S1 CG2D1O CG2DC1 CG NG2S1 CG2D1O CG2DC1 CG HGP1 NG2S1 CG2D1O CG2DC !dhb CG2D1O CG2DC1 CG331 HGA !dhb CG2DC1 CG2D1O CG2O1 OG2D !dhb CG2DC1 CG2D1O CG2O1 OG2D !dhb CG2DC1 CG2D1O CG2O1 OG2D !dhb CG2DC1 CG2D1O CG2O1 NG2S !dhb CG2DC1 CG2D1O CG2O1 NG2S !dhb CG2DC1 CG2D1O CG2O1 NG2S !dhb HGA4 CG2DC1 CG2D1O CG2O !dhb CG331 CG2DC1 CG2D1O CG2O !dhb c11c7c6c5 CG331 CG2DC1 CG2D1O CG2O CG331 CG2DC1 CG2D1O CG2O CG2DC2 CG2D1O CG2O1 NG2S !c7c6c5n10 CG2DC2 CG2D1O CG2O1 NG2S CG2DC2 CG2D1O CG2O1 NG2S CG2D1O NG2S1 CG2O1 CG !c2c4n8c6 CG2D1O NG2S1 CG2O1 CG CG2D1O NG2S1 CG2O1 CG CG2O1 CG2D1O NG2S1 CG2O CG2O1 CG2D1O NG2S1 CG2O
7 CG2O1 CG2D1O NG2S1 CG2O CG2O1 CG2D1O NG2S1 CG2O CG2DC3 CG2D1O NG2S1 CG2O CG2DC3 CG2D1O NG2S1 CG2O CG2DC3 CG2D1O NG2S1 CG2O CG2D1O CG2O1 NG2S1 CG CG2D1O CG2O1 NG2S1 CG CG2DC3 CG2D1O CG2O1 NG2S !c7c6c5n10 CG2DC3 CG2D1O CG2O1 NG2S CG2DC3 CG2D1O CG2O1 NG2S CG2DC3 CG2D1O CG2O1 OG2D !c7c6c509o9 CG2DC3 CG2D1O CG2O1 OG2D CG2DC3 CG2D1O CG2O1 OG2D NG2S1 CG2D1O CG2O1 NG2S !n8c6c5n10 NG2S1 CG2D1O CG2O1 NG2S NG2S1 CG2D1O CG2O1 NG2S NG2S1 CG2D1O CG2O1 OG2D !n8c6c5o9 NG2S1 CG2D1O CG2O1 OG2D NG2S1 CG2D1O CG2O1 OG2D CG2D1O NG2S1 CG2O1 OG2D !o3c4n8c6 CG2D1O NG2S1 CG2O1 OG2D CG2D1O NG2S1 CG2O1 OG2D ! For joining protein and CGen sets NH1 CT1 C NG2S CT1 C NG2S1 HGP CT1 C NG2S1 CG2D1O CT1 C NG2S1 CG2D1O HB1 CT1 C NG2S CT3 CT1 C NG2S C NG2S1 CG2D1O CG2DC C NG2S1 CG2D1O CG2DC C NG2S1 CG2D1O CG2DC C NG2S1 CG2D1O CG2O C NG2S1 CG2D1O CG2O C NG2S1 CG2D1O CG2O C NG2S1 CG2D1O CG2O O C NG2S1 HGP O C NG2S1 CG2D1O NG2S1 CG2D1O CG2O1 NH CG2D1O CG2O1 NH1 H CG2D1O CG2O1 NH1 CT CG2D1O CG2O1 NH1 CT CG2DC3 CG2D1O CG2O1 NH CG2DC3 CG2D1O CG2O1 NH CG2DC3 CG2D1O CG2O1 NH CG2O1 NH1 CT1 HB CG2O1 NH1 CT1 CT CG2O1 NH1 CT1 C OG2D1 CG2O1 NH1 H OG2D1 CG2O1 NH1 CT C NG2S1 CG2D1O CG2DC C NG2S1 CG2D1O CG2DC C NG2S1 CG2D1O CG2DC CG2DC1 CG2D1O CG2O1 NH CG2DC1 CG2D1O CG2O1 NH CG2DC1 CG2D1O CG2O1 NH CT1 CT1 C NG2S CG2D1O CG2O1 NH1 CTD CG2D1O CG2O1 NH1 CTD CG2O1 NH1 CTD1 HB
8 CG2O1 NH1 CTD1 CT CG2O1 NH1 CTD1 C OG2D1 CG2O1 NH1 CTD CG2O1 NH1 CT1 CT NH3 CT1 C NG2S CG2O1 NH1 CT1 CC CG2O1 NH1 CTD1 CT CTD1 CT2 S CT ! from CT3 CT2 S CT3 CTD1 CT2 S CT ! from CT3 CT2 S CT3 CT2 S CT2 CT ! from CT3 CT2 S CT3 CT2 S CT2 CT ! from CT3 CT2 S CT3 CT2 S CT2 HA ! from HA2 CT2 S CT3 CT3 CT2 S CT ! from CT3 CT2 S CT3 CT3 CT2 S CT ! from CT3 CT2 S CT3 IMPROPERS CG2D1O CG2DC3 CG2O1 NG2S ! Molecule, from CG2O5 CG2O3 CG2R61 OG2D3 CG2O1 CG2D1O NG2S1 OG2D ! Molecule, from CG2O1 CG2DC1 NG2S1 OG2D1 CG2D1O CG2DC1 CG2O1 NG2S ! Molecule, from CG2O5 CG2O3 CG2R61 OG2D3 CG2O1 CG2D1O NH1 OG2D CMAP!! CMAP terms to allow DHAR and DHAB to be included in the peptide chain. CMAP is not applied to the!! non-standard residues, but definition of phi and psi is changed for neighborous due to different atom!! type names in CGEN and protein parameter sets. C NH1 CT1 C NH1 CT1 C NG2S1 24! phi = ! phi = ! phi = ! phi =
9 ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
10 ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = 135.0
11 ! phi = ! phi = CG2O1 NH1 CT1 C NH1 CT1 C NH1 24! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
12 ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
13 ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
14 ! phi = CG2O1 NH1 CT1 C NH1 CT1 C NG2S1 24! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
15 ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
16 ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi = ! phi =
17 CG2O1 NH1 CTD1 C NH1 CTD1 C NH1 24! ! ! ! ! ! !-90!-75!
18 !-45!-30!-15!0!15!30!45!
19 !75!90!105!120!135!150! END RETURN
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