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top_martini_in_charmm_davide.rtf
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top_martini_in_charmm_davide.rtf
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!
! MARTINI FORCE FIELD FOR CG SIMULATIONS
! IN CHARMM FORM FOR LAMMPS
!
! TOPOLOGY FILE
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! !
! Francesca Collu e Enrico Spiga !
! ultima modifica 26-01-2009 !
! !
! Davide Alemani !
! last modified 30-06-2009 !
! Added 1 molecule of water as !
! W1 (atom type) in MASS !
! WAT (residue type) in RESI !
! !
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
31 1
!
!
! template
! standard backbones and special backbones
MASS 1 P5p 57.05400 ! bead aminoacids
MASS 2 Qdb 57.05400 ! amino-terminal aminoacids
MASS 3 Qab 72.04600 ! carboxi-terminal aminoacids
MASS 4 P5G 57.05400 ! glycine (only one bead)
MASS 5 P4A 72.08800 ! alanine (only one bead)
MASS 6 NaP 57.05400 ! backbone proline
! side chains
MASS 7 C5C 47.09400 ! cysteine
MASS 8 ACV 43.08600 ! valine
MASS 9 ACL 57.11200 ! leucine and isoleucine
MASS 10 C5M 75.14600 ! methionine
MASS 11 P5N 58.06200 ! asparagine
MASS 12 P4Q 72.08800 ! glutamine
MASS 13 QaD 58.03600 ! aspartate
MASS 14 QaE 73.07000 ! glutamate
MASS 15 P1T 45.06000 ! threonine
MASS 16 P1S 31.03400 ! serine
MASS 17 C3p 42.07800 ! SC1 lysine
MASS 18 QdK 31.0600 ! SC2 lysine
MASS 19 N0p 57.09600 ! SC1 arginine
MASS 20 QdR 44.06200 ! SC2 arginine
MASS 21 SCp 26.03600 ! SC1 histidine and phenylalanine
MASS 22 SPH 27.02800 ! SC2/SC3 histidine
MASS 23 SCF 32.54500 ! SC2/SC3 phenylalanine, tyrosine and tryptophan
MASS 24 SPY 43.04400 ! SC3 tyrosine
MASS 25 SCW 38.04600 ! SC1 tryptophan
MASS 26 SPW 27.02800 ! SC2 tryptophan
MASS 27 ACP 43.09
! water
MASS 28 P4 72.00000 ! water (4 in 1)
MASS 29 BP4 72.00000 ! anti freeze water (4 in 1)
MASS 30 W1 16.00000 ! 1 molecule of water
!
DECL -BN0
DECL +BN0
! la riga di sotto serve?
!DEFA FIRS NTER LAST CTER
AUTO ANGLES DIHE
! water (original from MARTINI)
RESI W 0.00
GROUP
ATOM W P4 0.0
! anti freeze water (original from MARTINI)
RESI WF 0.00
GROUP
ATOM WF BP4 0.0
! water (1 molecule)
RESI WAT 0.00
GROUP
ATOM W1 W1 0.0
! ala
RESI ALA 0.00
GROUP
ATOM BN0 P4A 0.0 ! |
! HN-N
! | HB1
! | /
! HA-CA--CB-HB2
! | \
! | HB3
! O=C
! |
!
BOND BN0 +BN0
! ala n-terminal
RESI ALAN 1.00
GROUP
ATOM BN0 Qdb 1.0
! H
! |
! H-N-H
! | HB1
! | /
! HA-CA--CB-HB2
! | \
! | HB3
! O=C
! |
!
BOND BN0 +BN0
! ala c-terminal
RESI ALAC -1.00
GROUP
ATOM BN0 Qab -1.0
! |
! H-N-H
! | HB1
! | /
! HA-CA--CB-HB2
! | \
! | HB3
! O=C-O-
!
BOND BN0 +BN0
! arg
RESI ARG 1.00
GROUP
ATOM BN0 P5p 0.0 ! | HH11
ATOM SC1 N0p 0.0 ! HN-N |
ATOM SC2 QdR 1.0 ! | HB1 HG1 HD1 HE NH1-HH12
! | | | | | //(+)
! HA-CA--CB--CG--CD--NE--CZ
! | | | | \
! | HB2 HG2 HD2 NH2-HH22
! O=C |
! | HH21
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
! arg n-terminal
RESI ARGN 2.00
GROUP
ATOM BN0 Qdb 1.0 ! | HH11
ATOM SC1 N0p 0.0 ! HN-N |
ATOM SC2 QdR 1.0 ! | HB1 HG1 HD1 HE NH1-HH12
! | | | | | //(+)
! HA-CA--CB--CG--CD--NE--CZ
! | | | | \
! | HB2 HG2 HD2 NH2-HH22
! O=C |
! | HH21
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
! arg c-terminal
RESI ARGC 0.00
GROUP
ATOM BN0 Qab -1.0 ! | HH11
ATOM SC1 N0p 0.0 ! HN-N |
ATOM SC2 QdR 1.0 ! | HB1 HG1 HD1 HE NH1-HH12
! | | | | | //(+)
! HA-CA--CB--CG--CD--NE--CZ
! | | | | \
! | HB2 HG2 HD2 NH2-HH22
! O=C |
! | HH21
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
! asn
RESI ASN 0.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 P5N 0.0 ! HN-N
! | HB1 OD1 HD21 (cis to OD1)
! | | || /
! HA-CA--CB--CG--ND2
! | | \
! | HB2 HD22 (trans to OD1)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! asn n-terminal
RESI ASNN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 P5N 0.0 ! HN-N
! | HB1 OD1 HD21 (cis to OD1)
! | | || /
! HA-CA--CB--CG--ND2
! | | \
! | HB2 HD22 (trans to OD1)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! asn c-terminal
RESI ASNC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 P5N 0.0 ! HN-N
! | HB1 OD1 HD21 (cis to OD1)
! | | || /
! HA-CA--CB--CG--ND2
! | | \
! | HB2 HD22 (trans to OD1)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! asp
RESI ASP -1.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 QaD -1.0 ! HN-N
! | HB1 OD1
! | | //
! HA-CA--CB--CG
! | | \
! | HB2 OD2(-)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! asp n-terminal
RESI ASPN 0.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 QaD -1.0 ! HN-N
! | HB1 OD1
! | | //
! HA-CA--CB--CG
! | | \
! | HB2 OD2(-)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! asp c-terminal
RESI ASPC -2.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 QaD -1.0 ! HN-N
! | HB1 OD1
! | | //
! HA-CA--CB--CG
! | | \
! | HB2 OD2(-)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! asp neutral form
RESI ASP0 0.0
GROUP
ATOM BN0 P5p
ATOM SC1 P3D
! cys
RESI CYS 0.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 C5C 0.0 ! HN-N
! | HB1
! | |
! HA-CA--CB--SG
! | | \
! | HB2 HG1
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! cys n-terminal
RESI CYSN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 C5C 0.0 ! HN-N
! | HB1
! | |
! HA-CA--CB--SG
! | | \
! | HB2 HG1
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! cys c-terminal
RESI CYSC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 C5C 0.0 ! HN-N
! | HB1
! | |
! HA-CA--CB--SG
! | | \
! | HB2 HG1
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! gln
RESI GLN 0.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 P4Q 0.0 ! HN-N
! | HB1 HG1 OE1 HE21 (cis to OE1)
! | | | || /
! HA-CA--CB--CG--CD--NE2
! | | | \
! | HB2 HG2 HE22 (trans to OE1)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! gln n-terminal
RESI GLNN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 P4Q 0.0 ! HN-N
! | HB1 HG1 OE1 HE21 (cis to OE1)
! | | | || /
! HA-CA--CB--CG--CD--NE2
! | | | \
! | HB2 HG2 HE22 (trans to OE1)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! gln c-terminal
RESI GLNC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 P4Q 0.0 ! HN-N
! | HB1 HG1 OE1 HE21 (cis to OE1)
! | | | || /
! HA-CA--CB--CG--CD--NE2
! | | | \
! | HB2 HG2 HE22 (trans to OE1)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! glu
RESI GLU -1.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 QaE -1.0 ! HN-N
! | HB1 HG1 OE1
! | | | //
! HA-CA--CB--CG--CD
! | | | \
! | HB2 HG2 OE2(-)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! glu n-terminal
RESI GLUN 0.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 QaE -1.0 ! HN-N
! | HB1 HG1 OE1
! | | | //
! HA-CA--CB--CG--CD
! | | | \
! | HB2 HG2 OE2(-)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! glu c-terminal
RESI GLUC -2.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 QaE -1.0 ! HN-N
! | HB1 HG1 OE1
! | | | //
! HA-CA--CB--CG--CD
! | | | \
! | HB2 HG2 OE2(-)
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! gly
RESI GLY 0.00
GROUP
ATOM BN0 P5G 0.0 ! |
! N-H
! |
! |
! HA1-CA-HA2
! |
! |
! C=O
! |
BOND BN0 +BN0
! gly n-terminal
RESI GLYN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
! N-H
! |
! |
! HA1-CA-HA2
! |
! |
! C=O
! |
BOND BN0 +BN0
! gly c-terminal
RESI GLYC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
! N-H
! |
! |
! HA1-CA-HA2
! |
! |
! C=O
! |
BOND BN0 +BN0
! histidine (no difference between protonation state)
RESI HSD 0.00 ! neutral HIS, proton on ND1
GROUP
ATOM BN0 P5p 0.0 ! | HD1 HE1
ATOM SC1 SCp 0.0 ! HN-N | /
ATOM SC2 SPH 0.0 ! | HB1 ND1--CE1
ATOM SC3 SPH 0.0 ! | | / ||
! HA-CA--CB--CG ||
! | | \\ ||
! | HB2 CD2--NE2
! O=C |
! | HD2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! histidine n-terminal (no difference between protonation state)
RESI HSDN 1.00 ! neutral HIS, proton on ND1
GROUP
ATOM BN0 Qdb 1.0 ! | HD1 HE1
ATOM SC1 SCp 0.0 ! HN-N | /
ATOM SC2 SPH 0.0 ! | HB1 ND1--CE1
ATOM SC3 SPH 0.0 ! | | / ||
! HA-CA--CB--CG ||
! | | \\ ||
! | HB2 CD2--NE2
! O=C |
! | HD2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! histidine c-terminal (no difference between protonation state)
RESI HSDC -1.00 ! neutral HIS, proton on ND1
GROUP
ATOM BN0 Qab -1.0 ! | HD1 HE1
ATOM SC1 SCp 0.0 ! HN-N | /
ATOM SC2 SPH 0.0 ! | HB1 ND1--CE1
ATOM SC3 SPH 0.0 ! | | / ||
! HA-CA--CB--CG ||
! | | \\ ||
! | HB2 CD2--NE2
! O=C |
! | HD2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! ile
RESI ILE 0.00
GROUP
ATOM BN0 P5p 0.0 ! | HG21 HG22
ATOM SC1 ACL 0.0 ! HN-N | /
! | CG2--HG23
! | /
! HA-CA--CB-HB HD1
! | \ /
! | CG1--CD--HD2
! O=C / \ \
! | HG11 HG12 HD3
BOND BN0 +BN0
BOND BN0 SC1
! ile n-terminal
RESI ILEN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! | HG21 HG22
ATOM SC1 ACL 0.0 ! HN-N | /
! | CG2--HG23
! | /
! HA-CA--CB-HB HD1
! | \ /
! | CG1--CD--HD2
! O=C / \ \
! | HG11 HG12 HD3
BOND BN0 +BN0
BOND BN0 SC1
! ile c-terminal
RESI ILEC -1.00
GROUP
ATOM BN0 Qab -1.0 ! | HG21 HG22
ATOM SC1 ACL 0.0 ! HN-N | /
! | CG2--HG23
! | /
! HA-CA--CB-HB HD1
! | \ /
! | CG1--CD--HD2
! O=C / \ \
! | HG11 HG12 HD3
BOND BN0 +BN0
BOND BN0 SC1
! leu
RESI LEU 0.00
GROUP
ATOM BN0 P5p 0.0 ! | HD11 HD12
ATOM SC1 ACL 0.0 ! HN-N | /
! | HB1 CD1--HD13
! | | /
! HA-CA--CB--CG-HG
! | | \
! | HB2 CD2--HD23
! O=C | \
! | HD21 HD22
BOND BN0 +BN0
BOND BN0 SC1
! leu n-terminal
RESI LEUN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! | HD11 HD12
ATOM SC1 ACL 0.0 ! HN-N | /
! | HB1 CD1--HD13
! | | /
! HA-CA--CB--CG-HG
! | | \
! | HB2 CD2--HD23
! O=C | \
! | HD21 HD22
BOND BN0 +BN0
BOND BN0 SC1
! leu c-terminal
RESI LEUC -1.00
GROUP
ATOM BN0 Qab -1.0 ! | HD11 HD12
ATOM SC1 ACL 0.0 ! HN-N | /
! | HB1 CD1--HD13
! | | /
! HA-CA--CB--CG-HG
! | | \
! | HB2 CD2--HD23
! O=C | \
! | HD21 HD22
BOND BN0 +BN0
BOND BN0 SC1
! lys
RESI LYS 1.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 C3p 0.0 ! HN-N
ATOM SC2 QdK 1.0 ! | HB1 HG1 HD1 HE1 HZ1
! | | | | | /
! HA-CA--CB--CG--CD--CE--NZ--HZ2
! | | | | | \
! | HB2 HG2 HD2 HE2 HZ3
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
! lys n-terminal
RESI LYSN 2.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 C3p 0.0 ! HN-N
ATOM SC2 QdK 1.0 ! | HB1 HG1 HD1 HE1 HZ1
! | | | | | /
! HA-CA--CB--CG--CD--CE--NZ--HZ2
! | | | | | \
! | HB2 HG2 HD2 HE2 HZ3
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
! lys c-terminal
RESI LYSC 0.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 C3p 0.0 ! HN-N
ATOM SC2 QdK 1.0 ! | HB1 HG1 HD1 HE1 HZ1
! | | | | | /
! HA-CA--CB--CG--CD--CE--NZ--HZ2
! | | | | | \
! | HB2 HG2 HD2 HE2 HZ3
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
! met
RESI MET 0.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 C5M 0.0 ! HN-N
! | HB1 HG1 HE1
! | | | |
! HA-CA--CB--CG--SD--CE--HE3
! | | | |
! | HB2 HG2 HE2
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! met n-terminal
RESI METN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 C5M 0.0 ! HN-N
! | HB1 HG1 HE1
! | | | |
! HA-CA--CB--CG--SD--CE--HE3
! | | | |
! | HB2 HG2 HE2
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! met c-terminal
RESI METC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 C5M 0.0 ! HN-N
! | HB1 HG1 HE1
! | | | |
! HA-CA--CB--CG--SD--CE--HE3
! | | | |
! | HB2 HG2 HE2
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! phe
RESI PHE 0.00
GROUP
ATOM BN0 P5p 0.0 ! | HD1 HE1
ATOM SC1 SCp 0.0 ! HN-N | |
ATOM SC2 SCF 0.0 ! | HB1 CD1--CE1
ATOM SC3 SCF 0.0 ! | | // \\
! HA-CA--CB--CG CZ--HZ
! | | \ __ /
! | HB2 CD2--CE2
! O=C | |
! | HD2 HE2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! phe n-terminal
RESI PHEN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! | HD1 HE1
ATOM SC1 SCp 0.0 ! HN-N | |
ATOM SC2 SCF 0.0 ! | HB1 CD1--CE1
ATOM SC3 SCF 0.0 ! | | // \\
! HA-CA--CB--CG CZ--HZ
! | | \ __ /
! | HB2 CD2--CE2
! O=C | |
! | HD2 HE2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! phe c-terminal
RESI PHEC -1.00
GROUP
ATOM BN0 Qdb -1.0 ! | HD1 HE1
ATOM SC1 SCp 0.0 ! HN-N | |
ATOM SC2 SCF 0.0 ! | HB1 CD1--CE1
ATOM SC3 SCF 0.0 ! | | // \\
! HA-CA--CB--CG CZ--HZ
! | | \ __ /
! | HB2 CD2--CE2
! O=C | |
! | HD2 HE2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! pro
RESI PRO 0.00
GROUP ! HD1 HD2
ATOM BN0 NaP 0.0 ! | \ /
ATOM SC1 ACP 0.0 ! N---CD HG1 ATOM CA CP1 0.02
! | \ /
! | CG
! | / \
! HA-CA--CB HG2
! | / \
! | HB1 HB2
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! pro n-terminal
RESI PRON 1.00
GROUP ! HD1 HD2
ATOM BN0 Qdb 1.0 ! | \ /
ATOM SC1 ACP 0.0 ! N---CD HG1 ATOM CA CP1 0.02
! | \ /
! | CG
! | / \
! HA-CA--CB HG2
! | / \
! | HB1 HB2
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! pro c-terminal
RESI PROC -1.00
GROUP ! HD1 HD2
ATOM BN0 Qab -1.0 ! | \ /
ATOM SC1 ACP 0.0 ! N---CD HG1 ATOM CA CP1 0.02
! | \ /
! | CG
! | / \
! HA-CA--CB HG2
! | / \
! | HB1 HB2
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! ser
RESI SER 0.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 P1S 0.0 ! HN-N
! | HB1
! | |
! HA-CA--CB--OG
! | | \
! | HB2 HG1
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! ser n-terminal
RESI SERN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 P1S 0.0 ! HN-N
! | HB1
! | |
! HA-CA--CB--OG
! | | \
! | HB2 HG1
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! ser c-terminal
RESI SERC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 P1S 0.0 ! HN-N
! | HB1
! | |
! HA-CA--CB--OG
! | | \
! | HB2 HG1
! O=C
! |
BOND BN0 +BN0
BOND BN0 SC1
! thr
RESI THR 0.00
GROUP
ATOM BN0 P5p 0.0 ! |
ATOM SC1 P1T 0.0 ! HN-N
! | OG1--HG1
! | /
! HA-CA--CB-HB
! | \
! | CG2--HG21
! O=C / \
! | HG21 HG22
BOND BN0 +BN0
BOND BN0 SC1
! thr n-terminal
RESI THRN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! |
ATOM SC1 P1T 0.0 ! HN-N
! | OG1--HG1
! | /
! HA-CA--CB-HB
! | \
! | CG2--HG21
! O=C / \
! | HG21 HG22
BOND BN0 +BN0
BOND BN0 SC1
! thr c-terminal
RESI THRC -1.00
GROUP
ATOM BN0 Qab -1.0 ! |
ATOM SC1 P1T 0.0 ! HN-N
! | OG1--HG1
! | /
! HA-CA--CB-HB
! | \
! | CG2--HG21
! O=C / \
! | HG21 HG22
BOND BN0 +BN0
BOND BN0 SC1
! trp
RESI TRP 0.00
GROUP
ATOM BN0 P5p 0.0 ! | HE3
ATOM SC1 SCW 0.0 ! HN-N |
ATOM SC2 SPW 0.0 ! | HB1 CE3
ATOM SC3 SCF 0.0 ! | | / \\
ATOM SC4 SCF 0.0 ! HA-CA--CB---CG-----CD2 CZ3-HZ3
! | | || || |
! | HB2 CD1 CE2 CH2-HH2
! O=C / \ / \ //
! | HD1 NE1 CZ2
! | |
! HE1 HZ2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC2 SC3
BOND SC1 SC3
BOND SC2 SC4
BOND SC3 SC4
! trp n-terminal
RESI TRPN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! | HE3
ATOM SC1 SCW 0.0 ! HN-N |
ATOM SC2 SPW 0.0 ! | HB1 CE3
ATOM SC3 SCF 0.0 ! | | / \\
ATOM SC4 SCF 0.0 ! HA-CA--CB---CG-----CD2 CZ3-HZ3
! | | || || |
! | HB2 CD1 CE2 CH2-HH2
! O=C / \ / \ //
! | HD1 NE1 CZ2
! | |
! HE1 HZ2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC2 SC3
BOND SC1 SC3
BOND SC2 SC4
BOND SC3 SC4
! trp c-terminal
RESI TRPC -1.00
GROUP
ATOM BN0 Qab -1.0 ! | HE3
ATOM SC1 SCW 0.0 ! HN-N |
ATOM SC2 SPW 0.0 ! | HB1 CE3
ATOM SC3 SCF 0.0 ! | | / \\
ATOM SC4 SCF 0.0 ! HA-CA--CB---CG-----CD2 CZ3-HZ3
! | | || || |
! | HB2 CD1 CE2 CH2-HH2
! O=C / \ / \ //
! | HD1 NE1 CZ2
! | |
! HE1 HZ2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC2 SC3
BOND SC1 SC3
BOND SC2 SC4
BOND SC3 SC4
! tyr
RESI TYR 0.00
GROUP
ATOM BN0 P5p 0.0 ! | HD1 HE1
ATOM SC1 SCF 0.0 ! HN-N | |
ATOM SC2 SCF 0.0 ! | HB1 CD1--CE1
ATOM SC3 SPY 0.0 ! | | // \\
! HA-CA--CB--CG CZ--OH
! | | \ __ / \
! | HB2 CD2--CE2 HH
! O=C | |
! | HD2 HE2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! tyr n-terminal
RESI TYRN 1.00
GROUP
ATOM BN0 Qdb 1.0 ! | HD1 HE1
ATOM SC1 SCF 0.0 ! HN-N | |
ATOM SC2 SCF 0.0 ! | HB1 CD1--CE1
ATOM SC3 SPY 0.0 ! | | // \\
! HA-CA--CB--CG CZ--OH
! | | \ __ / \
! | HB2 CD2--CE2 HH
! O=C | |
! | HD2 HE2
BOND BN0 +BN0
BOND BN0 SC1
BOND SC1 SC2
BOND SC1 SC3
BOND SC2 SC3
! tyr c-terminal
RESI TYRC -1.00
GROUP
ATOM BN0 Qab -1.0 ! | HD1 HE1
ATOM SC1 SCF 0.0 ! HN-N | |
ATOM SC2 SCF 0.0 ! | HB1 CD1--CE1
ATOM SC3 SPY 0.0 ! | | // \\
! HA-CA--CB--CG CZ--OH
! | | \ __ / \
! | HB2 CD2--CE2 HH
! O=C | |
! | HD2 HE2
BOND BN0 +BN0