[gmx-users] (no subject)

[fatemeh ramezani]

HI DEAR USERS
I want to simulate collagen by OPLSAA. I added hydroxyprolin parameters as follow:

in .hdb file : 

HYP     5
1       5       HA      CA      N       C       CB
2       6       HB      CB      CG      CA
1       6       HG      CG      CD      CB
1       6       HD      CD      N       CG
1       4       HH      OH      CG      CD


in  aminoacids.c.tdb file:
[ HYP-COO- ]
[ replace ]
CA    CA    opls_285    12.011    -0.09
C    C    opls_271    12.011    0.7
O    O1    opls_272    15.9994    -0.8
OXT    O2    opls_272    15.9994    -0.8
[ add ]
2    8    O    C    CA    N
    opls_272    15.9994    -0.8
[ impropers ]
CA    O1    C    O2    improper_O_C_X_Y

[ HYP-ZWITTERION_COO- ]
[ replace ]
CA    CA    opls_246    12.011    0.13
C    C    opls_271    12.011    0.7
O    O1    opls_272    15.9994    -0.8
OXT    O2    opls_272    15.9994    -0.8
[ add ]
2    8    O    C    CA    N
    opls_272    15.9994    -0.8
[ impropers ]
CA    O1    C    O2    improper_O_C_X_Y



in  aminoacids.n.tdb file:

[ HYP-COO- ]
[ replace ]
CA    CA    opls_285    12.011    -0.09
C    C    opls_271    12.011    0.7
O    O1    opls_272    15.9994    -0.8
OXT    O2    opls_272    15.9994    -0.8
[ add ]
2    8    O    C    CA    N
    opls_272    15.9994    -0.8
[ impropers ]
CA    O1    C    O2    improper_O_C_X_Y

[ HYP-ZWITTERION_COO- ]
[ replace ]
CA    CA    opls_246    12.011    0.13
C    C    opls_271    12.011    0.7
O    O1    opls_272    15.9994    -0.8
OXT    O2    opls_272    15.9994    -0.8
[ add ]
2    8    O    C    CA    N
    opls_272    15.9994    -0.8
[ impropers ]
CA    O1    C    O2    improper_O_C_X_Y


in aminoacids.rtp file:
 [HYP]
 [ atoms ]
   N     opls_239    -0.140  1
   CA    opls_246     0.010  1
   HA    opls_140     0.060  1
   CB    opls_136    -0.120  2
   HB1   opls_140     0.060  2
   HB2   opls_140     0.060  2  
   CG    opls_136    -0.120  3
   HG1   opls_140     0.060  3
   OH    opls_167    -0.683  3
   HH    opls_168     0.435  3  
   CD    opls_245    -0.050  4
   HD1   opls_140     0.060  4
   HD2   opls_140     0.060  4
   C     opls_235     0.500  5
   O     opls_236    -0.500  5
 [ bonds ]
   N     CA
   CA    HA
   CA    CB
   CA    C
   CB   HB1
   CB   HB2
   CB    CG
   CG   HG1
   CG    OH
   OH    HH
   CG    CD
   CD   HD1
   CD   HD2
   CD     N
    C     O
   -C     N
 [ impropers ]
   -C    CA     N    CD    improper_Z_N_X_Y
   CA    +N     C     O    improper_O_C_X_Y

in ffbonded.itp file:
[ angletypes ]
;  i    j    k  func       th0       cth
  CG     CB     OH      2   109.5      520.0
  OH     CG     CD      2   109.5      520.0 
  CG     OH     HH      2   109.5      450.0

[ dihedraltype ]
CG   CB   CD   OH     1    35.3  334.8           

CB   CG   OH   HH    1      0.0    1.3 3      


[ bondtype ]
CG   OH   2    0.144   6100000.0     ;    

OH   HH  2    0.100  15700000.0     ;    


 When I grompp, I get this error:
Unknown bond_atomtype HH
What does this error mean ?

 
Fatemeh Ramezani