*>>>>>> CHARMM topology for peptidoglycan <<<<<<
* Contains topology entries for NAG, NAM, d-gamma-glutamate (DGG), 
* and L-meso-diaminopimelic acid (DAP) and its amidated form (DAPA)
   36    1
MASS   174 CC3161  12.01100  C ! C2, C3, C4 CH bound to OH
MASS   175 CC3162  12.01100  C ! C1 (anomeric) CH bound to OH
MASS   176 CC3163  12.01100  C ! C5 CH bound to exocylic CH2OH
MASS   177 CC321   12.01100  C ! generic acyclic CH2 carbon (hexopyranose C6)
MASS   180 CC331   12.01100  C ! generic acyclic CH3 carbon (xyl C6, glcna/galna CT)
MASS   185 HCA1     1.00800  H ! aliphatic proton, CH
MASS   186 HCA2     1.00800  H ! aliphatic proton, CH2
MASS   187 HCA3     1.00800  H ! aliphatic proton, CH3
MASS   188 HCP1     1.00800  H ! polar H
MASS   191 OC311   15.99940  O ! hydroxyl oxygen
MASS   192 OC3C61  15.99940  O ! ether in six membered ring
MASS   193 OC301   15.99940  O ! generic linear ether

AUTOGENERATE angles dihedrals
! DEFAults for patching FIRSt and LAST residues
DEFA FIRS NONE LAST NONE

RESI NAG            0.000  ! N-Acetyl glucosamine
GROU                       !
ATOM C1   CC3162    0.340  !                  O6-HO6
ATOM H1   HCA1      0.090  !                  |
ATOM O1   OC311    -0.650  !              H61-C6-H62
ATOM HO1  HCP1      0.420  !                  |
ATOM C5   CC3163    0.110  !               H5-C5---O5
ATOM H5   HCA1      0.090  !            H4   /       \    O1-HO1
ATOM O5   OC3C61   -0.400  !              \ / HO3     \  /
GROU                       !               C4 |        C1
ATOM C2   CC3161    0.134  !              / \ O3   H2 /  \
ATOM H2   HCA1      0.090  !        HO4-O4   \|    | /    H1
GROU                       !                  C3---C2
ATOM C3   CC3161    0.140  !                  |    |
ATOM H3   HCA1      0.090  !                  H3   |...(acetamide)
ATOM O3   OC311    -0.650  !                       |
ATOM HO3  HCP1      0.420  !            HC1        |
GROU                       !               \       |
ATOM C4   CC3161    0.140  !          HC2--CC--CM--NC
ATOM H4   HCA1      0.090  !              /    ||   \
ATOM O4   OC311    -0.650  !           HC3     OM    HN
ATOM HO4  HCP1      0.420  !
GROU
ATOM C6   CC321     0.050
ATOM H61  HCA2      0.090
ATOM H62  HCA2      0.090
ATOM O6   OC311    -0.650
ATOM HO6  HCP1      0.420
GROU
ATOM CC   CT3       -0.27 
ATOM CM   CC         0.55 
ATOM NC   NH1       -0.587
ATOM HN   H          0.363 
ATOM OM   O         -0.55
ATOM HC1  HA         0.09
ATOM HC2  HA         0.09
ATOM HC3  HA         0.09
!
BOND C1   O1        C1   H1        O1   HO1       C1   O5        C1   C2
BOND C2   H2        C2   C3        C3   H3
BOND C3   O3        O3   HO3       C3   C4        C4   H4        C4   O4
BOND O4   HO4       C4   C5        C5   H5        C5   C6        C6   H61
BOND C6   H62       C6   O6        O6   HO6       C5   O5
!
BOND  CM NC   NC HN    NC C2
DOUBLE  CM   OM
BOND  CM   CC  CC  HC1 CC  HC2  CC  HC3
IMPR  CM  CC NC  OM   
IMPR  NC  CM  HN C2  
!    I    J    K    L      R(IK)   T(IKJ)    PHI   T(JKL)   R(KL)
IC   O1   C2  *C1   H1     1.3899  110.90  120.10  104.58   1.0836
IC   O1   O5  *C1   C2     1.3899  108.62  122.10  110.88   1.5316
IC   O2   C3  *C2   H2     1.4594  108.12 -118.78  111.06   1.1375
IC   O2   C1  *C2   C3     1.4594  115.65 -125.60  113.28   1.4983
IC   O3   C4  *C3   H3     1.4071  113.48  122.06  103.39   1.0895
IC   O3   C2  *C3   C4     1.4071  108.48  124.18  109.26   1.5497
IC   O4   C5  *C4   H4     1.3940  111.12 -110.35  108.66   1.0857
IC   O4   C3  *C4   C5     1.3940  112.77 -129.39  115.62   1.5530
IC   C6   O5  *C5   H5     1.5597  111.17  120.85  110.98   1.1092
IC   C6   C4  *C5   O5     1.5597  109.90  122.92  110.30   1.4512
IC   O6   H62 *C6   H61    1.4589  116.11 -112.93  103.57   1.1467
IC   O6   C5  *C6   H62    1.4589  109.41 -135.95  118.22   1.0853
IC   O5   C1   C2   C3     1.4620  110.88   57.82  113.28   1.4983
IC   C1   C2   C3   C4     1.5316  113.28  -48.40  109.26   1.5497
IC   C2   C3   C4   C5     1.4983  109.26   45.07  115.62   1.5530
IC   C3   C4   C5   O5     1.5497  115.62  -49.19  110.30   1.4512
IC   C4   C5   O5   C1     1.5530  110.30   56.36  112.12   1.4620
IC   C5   O5   C1   C2     1.4512  112.12  -61.39  110.88   1.5316
IC   C4   C5   C6   O6     1.5530  109.90 -177.46  109.41   1.4589
IC   O5   C1   O1   HO1    1.4620  108.62   72.25  106.48   0.9328
IC   C1   C2   O2   HO2    1.5316  115.65  135.41  116.81   0.9527
IC   C2   C3   O3   HO3    1.4983  108.48  -71.46  120.86   0.9441
IC   C3   C4   O4   HO4    1.5497  112.77   47.45  109.31   0.9911
IC   C5   C6   O6   HO6    1.5597  109.41  -54.60  118.82   0.95210
PATC  FIRS NONE LAST NONE


RESI NAM            0.000  ! N-Acetylmuramic acid, NAG + lactic acid 
GROU                       !
ATOM C1   CC3162    0.340  !                  O6-HO6                  
ATOM H1   HCA1      0.090  !                  |                       
ATOM O1   OC311    -0.650  !              H61-C6-H62                  
ATOM HO1  HCP1      0.420  !                  |                       
ATOM C5   CC3163    0.110  !               H5-C5---O5                 
ATOM H5   HCA1      0.090  !            H4   /       \    O1-HO1 
ATOM O5   OC3C61   -0.400  !              \ /         \  /           
GROU                       !               C4          C1            
ATOM C2   CC3161    0.134  !              / \ H3   H2 /  \           
ATOM H2   HCA1      0.090  !        HO4-O4   \|    | /    H1         
GROU                       !                  C3---C2                
ATOM C3   CC3161   -0.024  !   (lactic acid)  |    |                 
ATOM H3   HCA1      0.090  !          HB1    O3    |...(acetamide)   
ATOM O3   OC311    -0.406  !            \   /      |                  
GROU                       !       HB2--CB-CA-HA   |         HC1      
ATOM C4   CC3161    0.140  !           /   |       |         /        
ATOM H4   HCA1      0.090  !         HB3   C       NC---CM--CC--HC2   
ATOM O4   OC311    -0.650  !              / \\    /     ||   \        
ATOM HO4  HCP1      0.420  !            OE1  O   HN     OM   HC3          
GROU                       !             |
ATOM C6   CC321     0.050  !            HE1
ATOM H61  HCA2      0.090                                            
ATOM H62  HCA2      0.090
ATOM O6   OC311    -0.650
ATOM HO6  HCP1      0.420
GROU
ATOM CC   CT3       -0.27 
ATOM CM   CC         0.55 
ATOM NC   NH1       -0.587
ATOM HN   H          0.363 
ATOM OM   O         -0.55
ATOM HC1  HA         0.09
ATOM HC2  HA         0.09
ATOM HC3  HA         0.09
GROUP
ATOM CA   CT1        0.250
ATOM HA   HB         0.09
GROUP                    
ATOM CB   CT3       -0.27
ATOM HB1  HA         0.09
ATOM HB2  HA         0.09
ATOM HB3  HA         0.09
GROUP
ATOM C    CD      0.72  
ATOM O    OB     -0.55  
ATOM OE1  OH1    -0.61  
ATOM HE1  H       0.44
!
BOND C1   O1        C1   H1        O1   HO1       C1   O5        C1   C2
BOND C2   H2        C2   C3        C3   H3
BOND C3   O3        C3   C4        C4   H4        C4   O4
BOND O4   HO4       C4   C5        C5   H5        C5   C6        C6   H61
BOND C6   H62       C6   O6        O6   HO6       C5   O5
!
BOND  CM NC   NC HN    NC C2
DOUBLE  CM   OM
BOND  CM   CC  CC  HC1 CC  HC2  CC  HC3
!
BOND O3   CA        CA   HA        CA   C
BOND CA   CB        CB   HB1       CB   HB2       CB   HB3 
BOND C    OE1       OE1  HE1
DOUBLE C  O
IMPR  CM  CC NC  OM   
IMPR  NC  CM  HN C2  
!    I    J    K    L      R(IK)   T(IKJ)    PHI   T(JKL)   R(KL)
IC   O1   C2  *C1   H1     1.3899  110.90  120.10  104.58   1.0836
IC   O1   O5  *C1   C2     1.3899  108.62  122.10  110.88   1.5316
IC   O2   C3  *C2   H2     1.4594  108.12 -118.78  111.06   1.1375
IC   O2   C1  *C2   C3     1.4594  115.65 -125.60  113.28   1.4983
IC   O3   C4  *C3   H3     1.4071  113.48  122.06  103.39   1.0895
IC   O3   C2  *C3   C4     1.4071  108.48  124.18  109.26   1.5497
IC   O4   C5  *C4   H4     1.3940  111.12 -110.35  108.66   1.0857
IC   O4   C3  *C4   C5     1.3940  112.77 -129.39  115.62   1.5530
IC   C6   O5  *C5   H5     1.5597  111.17  120.85  110.98   1.1092
IC   C6   C4  *C5   O5     1.5597  109.90  122.92  110.30   1.4512
IC   O6   H62 *C6   H61    1.4589  116.11 -112.93  103.57   1.1467
IC   O6   C5  *C6   H62    1.4589  109.41 -135.95  118.22   1.0853
IC   O5   C1   C2   C3     1.4620  110.88   57.82  113.28   1.4983
IC   C1   C2   C3   C4     1.5316  113.28  -48.40  109.26   1.5497
IC   C2   C3   C4   C5     1.4983  109.26   45.07  115.62   1.5530
IC   C3   C4   C5   O5     1.5497  115.62  -49.19  110.30   1.4512
IC   C4   C5   O5   C1     1.5530  110.30   56.36  112.12   1.4620
IC   C5   O5   C1   C2     1.4512  112.12  -61.39  110.88   1.5316
IC   C4   C5   C6   O6     1.5530  109.90 -177.46  109.41   1.4589
IC   O5   C1   O1   HO1    1.4620  108.62   72.25  106.48   0.9328
IC   C1   C2   O2   HO2    1.5316  115.65  135.41  116.81   0.9527
IC   C2   C3   O3   HO3    1.4983  108.48  -71.46  120.86   0.9441
IC   C3   C4   O4   HO4    1.5497  112.77   47.45  109.31   0.9911
IC   C5   C6   O6   HO6    1.5597  109.41  -54.60  118.82   0.95210
PATC  FIRS NONE LAST NONE


RESI DGG         -1.00  ! D-gamma-glutamate
GROUP
ATOM N    NH1    -0.47  !     |
ATOM HN   H       0.31  !  HN-N
ATOM CA   CT1    -0.03  !     |     OE1
ATOM HA   HB      0.09  !     |   //
GROUP                   !  HA-CA--CD
ATOM CB   CT2    -0.18  !     |    \
ATOM HB1  HA      0.09  !     |     OE2(-)
ATOM HB2  HA      0.09  ! HB1-CB-HB2
GROUP                   !     |
ATOM CG   CT2    -0.18  !     |
ATOM HG1  HA      0.09  ! HG1-CG-HG2
ATOM HG2  HA      0.09  !     |
ATOM CD   CC      0.62  !     |
ATOM OE1  OC     -0.76  !     C==0
ATOM OE2  OC     -0.76  !     |
GROUP
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA  CG CB  CD CA  OE2 CD
BOND N  HN  N  CA  C  CG
BOND C  +N  CA HA  CB HB1 CB  HB2 CG  HG1
BOND CG HG2
DOUBLE O  C   CD  OE1
IMPR N   -C CA  HN  C CG +N O
IMPR CD CA OE2 OE1
!!CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N
ACCEPTOR OE1 CD
ACCEPTOR OE2 CD
ACCEPTOR O C


RESI DAP          0.00                                
GROUP                                                 
ATOM N    NH1    -0.47  !     |                   OZ1  
ATOM HN   H       0.31  !  HN-N                   ||   
ATOM CA   CT1     0.07  !     |   HB1 HG1 HD1     CZ--OZ2(-)
ATOM HA   HB      0.09  !     |   |   |   |       /     
GROUP                   !  HA-CA--CB--CG--CD----CE    HZ1 
ATOM CB   CT2    -0.18  !     |   |   |   |     | \  /  
ATOM HB1  HA      0.09  !     |   HB2 HG2 HD2  HE  NZ--HZ2 
ATOM HB2  HA      0.09  !   O=C                     \  
GROUP                   !     |                      HZ3+
ATOM CG   CT2    -0.18
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
GROUP
ATOM CD   CT2    -0.18
ATOM HD1  HA      0.09
ATOM HD2  HA      0.09
GROUP   !!taken from NTER
ATOM NZ   NH3    -0.30
ATOM HZ1  HC      0.33
ATOM HZ2  HC      0.33
ATOM HZ3  HC      0.33
ATOM CE   CT1     0.21
ATOM HE   HB      0.10
GROUP   !!taken from CTER
ATOM CZ   CC      0.34
ATOM OZ1  OC     -0.67
ATOM OZ2  OC     -0.67
GROUP
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   CG CB   CD CG   CE CD   NZ CE
BOND N  HN   N  CA    C  CA
BOND C  +N   CA HA   CB HB1  CB HB2  CG HG1
BOND CG HG2  CD HD1  CD HD2  CE HE   
BOND CE CZ   CZ OZ2
DOUBLE   O  C  CZ OZ1
BOND NZ HZ1  NZ HZ2  NZ HZ3
IMPR N -C CA HN  C CA +N O
IMPR CZ CE OZ2 OZ1
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N
DONOR HZ1 NZ
DONOR HZ2 NZ
DONOR HZ3 NZ
ACCEPTOR O C
IC -C   CA   *N   HN    1.3482 123.5700  180.0000 115.1100  0.9988
IC -C   N    CA   C     1.3482 123.5700  180.0000 107.2900  1.5187
IC N    CA   C    +N    1.4504 107.2900  180.0000 117.2700  1.3478
IC +N   CA   *C   O     1.3478 117.2700  180.0000 120.7900  1.2277
IC CA   C    +N   +CA   1.5187 117.2700  180.0000 124.9100  1.4487
IC N    C    *CA  CB    1.4504 107.2900  122.2300 111.3600  1.5568
IC N    C    *CA  HA    1.4504 107.2900 -116.8800 107.3600  1.0833
IC N    CA   CB   CG    1.4504 111.4700  180.0000 115.7600  1.5435
IC CG   CA   *CB  HB1   1.5435 115.7600  120.9000 107.1100  1.1146
IC CG   CA   *CB  HB2   1.5435 115.7600 -124.4800 108.9900  1.1131
IC CA   CB   CG   CD    1.5568 115.7600  180.0000 113.2800  1.5397
IC CD   CB   *CG  HG1   1.5397 113.2800  120.7400 109.1000  1.1138
IC CD   CB   *CG  HG2   1.5397 113.2800 -122.3400 108.9900  1.1143
IC CB   CG   CD   CE    1.5435 113.2800  180.0000 112.3300  1.5350
IC CE   CG   *CD  HD1   1.5350 112.3300  122.2500 108.4100  1.1141
IC CE   CG   *CD  HD2   1.5350 112.3300 -121.5900 108.1300  1.1146
IC CG   CD   CE   NZ    1.5397 112.3300  180.0000 110.4600  1.4604
IC NZ   CD   *CE  HE    1.4604 110.4600  119.9100 110.5100  1.1128
IC CD   CE   NZ   HZ1   1.5350 110.4600  179.9200 110.0200  1.0404
IC HZ1  CE   *NZ  HZ2   1.0404 110.0200  120.2700 109.5000  1.0402
IC HZ1  CE   *NZ  HZ3   1.0404 110.0200 -120.1300 109.4000  1.0401
IC NZ   CE   CZ   OZ2   0.0000  0.0000  180.0000  0.0000  0.0000
IC OZ2  CE   *CZ  OZ1   0.0000  0.0000  180.0000  0.0000  0.0000


RESI DAPA         1.00                                
GROUP                                                 
ATOM N    NH1    -0.47  !     |                   OZ    HT1
ATOM HN   H       0.31  !  HN-N                   ||   /
ATOM CA   CT1     0.07  !     |   HB1 HG1 HD1     CZ--NT--HT2   
ATOM HA   HB      0.09  !     |   |   |   |       /     
GROUP                   !  HA-CA--CB--CG--CD----CE    HZ1 
ATOM CB   CT2    -0.18  !     |   |   |   |     | \  /  
ATOM HB1  HA      0.09  !     |   HB2 HG2 HD2  HE  NZ--HZ2 
ATOM HB2  HA      0.09  !   O=C                     \  
GROUP                   !     |                      HZ3+
ATOM CG   CT2    -0.18
ATOM HG1  HA      0.09
ATOM HG2  HA      0.09
GROUP
ATOM CD   CT2    -0.18
ATOM HD1  HA      0.09
ATOM HD2  HA      0.09
GROUP   !!taken from NTER
ATOM NZ   NH3    -0.30
ATOM HZ1  HC      0.33
ATOM HZ2  HC      0.33
ATOM HZ3  HC      0.33
ATOM CE   CT1     0.21
ATOM HE   HB      0.10
GROUP   !!taken from CT2
ATOM CZ   CC      0.55
ATOM OZ   O      -0.55
ATOM NT   NH2    -0.62
ATOM HT1  H       0.32
ATOM HT2  H       0.30
GROUP
ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   CG CB   CD CG   CE CD   NZ CE
BOND N  HN   N  CA    C  CA
BOND C  +N   CA HA   CB HB1  CB HB2  CG HG1
BOND CG HG2  CD HD1  CD HD2  CE HE   
BOND CE CZ   CZ OZ   CZ NT   NT HT1  NT HT2
DOUBLE   O  C
BOND NZ HZ1  NZ HZ2  NZ HZ3
IMPR N -C CA HN     C CA +N O
IMPR CZ NT CE OZ    CZ CE NT OZ
IMPR NT CZ HT1 HT2  NT CZ HT2 HT1
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N
DONOR HZ1 NZ
DONOR HZ2 NZ
DONOR HZ3 NZ
DONOR HT1 NT
DONOR HT2 NT
ACCEPTOR O C
IC -C   CA   *N   HN    1.3482 123.5700  180.0000 115.1100  0.9988
IC -C   N    CA   C     1.3482 123.5700  180.0000 107.2900  1.5187
IC N    CA   C    +N    1.4504 107.2900  180.0000 117.2700  1.3478
IC +N   CA   *C   O     1.3478 117.2700  180.0000 120.7900  1.2277
IC CA   C    +N   +CA   1.5187 117.2700  180.0000 124.9100  1.4487
IC N    C    *CA  CB    1.4504 107.2900  122.2300 111.3600  1.5568
IC N    C    *CA  HA    1.4504 107.2900 -116.8800 107.3600  1.0833
IC N    CA   CB   CG    1.4504 111.4700  180.0000 115.7600  1.5435
IC CG   CA   *CB  HB1   1.5435 115.7600  120.9000 107.1100  1.1146
IC CG   CA   *CB  HB2   1.5435 115.7600 -124.4800 108.9900  1.1131
IC CA   CB   CG   CD    1.5568 115.7600  180.0000 113.2800  1.5397
IC CD   CB   *CG  HG1   1.5397 113.2800  120.7400 109.1000  1.1138
IC CD   CB   *CG  HG2   1.5397 113.2800 -122.3400 108.9900  1.1143
IC CB   CG   CD   CE    1.5435 113.2800  180.0000 112.3300  1.5350
IC CE   CG   *CD  HD1   1.5350 112.3300  122.2500 108.4100  1.1141
IC CE   CG   *CD  HD2   1.5350 112.3300 -121.5900 108.1300  1.1146
IC CG   CD   CE   NZ    1.5397 112.3300  180.0000 110.4600  1.4604
IC NZ   CD   *CE  HE    1.4604 110.4600  119.9100 110.5100  1.1128
IC CD   CE   NZ   HZ1   1.5350 110.4600  179.9200 110.0200  1.0404
IC HZ1  CE   *NZ  HZ2   1.0404 110.0200  120.2700 109.5000  1.0402
IC HZ1  CE   *NZ  HZ3   1.0404 110.0200 -120.1300 109.4000  1.0401
IC NZ   CE   CZ   OZ    0.0000  0.0000  180.0000  0.0000  0.0000
IC NT   CE   *CZ  OZ    0.0000  0.0000  180.0000  0.0000  0.0000  
IC CE   CZ   NT   HT1   0.0000  0.0000  180.0000  0.0000  0.0000
IC HT1  CZ   *NT  HT2   0.0000  0.0000  180.0000  0.0000  0.0000

! link NAM <-> NAG
PRES 14bb           0.02 ! (i)1->4(i-1) equatorial at C1 and equatorial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC3161    0.09 !
ATOM 1O4  OC301    -0.36 !
ATOM 2C1  CC3162    0.29 !
BOND 1O4  2C1
!    I    J    K    L      R(IK)   T(IKJ)    PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C1    1.5009  110.76   81.86  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O5    1.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C2    1.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H1    1.4470  108.63  121.92  111.32   1.0837


PRES CNAM         0.00 !
DELETE ATOM HO1  ! 0.42
GROUP
ATOM C1   CC3162  0.29 ! 0.340 
ATOM O1   OC301  -0.35 ! -0.65  
ATOM CT1  CC331  -0.10 !
ATOM HT1  HCA3    0.09 !
ATOM HT2  HCA3    0.09 !
ATOM HT3  HCA3    0.09 !
BOND O1 CT1
BOND CT1 HT1 CT1 HT2 CT1 HT3


! bond NAM -> ALA
PRES LPG         0.00
DELETE ATOM 1OE1     ! +0.61
DELETE ATOM 1HE1     ! -0.44
ATOM 1C   C     0.51 !   0.72  -.21
ATOM 1O   O    -0.51 !  -0.55  +.04
BOND 1C 2N
CMAP 1C 2N 2CA 2C   1N 1CA 1C 2N
IMPR 1C 1CA 2N 1O


! bond DAP -> ALA
PRES LNK3        -1.00
ATOM 1CE  CT1     0.07
ATOM 1HE  HB      0.09
ATOM 1NZ  NH1    -0.47
ATOM 1HZ1 H       0.31
BOND 1NZ  2C
DELETE ATOM 1HZ2
DELETE ATOM 1HZ3
IMPR 1NZ 2C 1CE 1HZ1  2C 2CA 1NZ 2O
CMAP 2C  1NZ  1CE  1CZ   2N  2CA  2C  1NZ
