[gmx-users] (no subject)

[Mohsen Ramezanpour]

Hi
I think you should use the correct atomtype, accoding to this FF
atomtypes, for your atom which you have introduced as HH.

Best
Mohsen


On Tue, Nov 19, 2013 at 7:48 PM, fatemeh ramezani <fr_750 at yahoo.com> wrote:

> 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
> --
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