On 11/19/13 11:31 AM, Mohsen Ramezanpour wrote:
Hi
I think you should use the correct atomtype, accoding to this FF
atomtypes, for your atom which you have introduced as HH.


Correct. More explicitly, the trick to dealing with OPLS-AA is that its nonbonded types (opls_*) have bonded equivalents that are defined in ffnonbonded.itp. The problem with the [ *types ] directives shown below is (first) that they use atom names instead of types and (second) that the strings are interpreted as types and do not correspond to the desired parameters.

The atom named "HH" has a nonbonded type opls_168, so its bonded type (thus what must be used in ffbonded.itp when defining interactions is "HO," not "HH."

-Justin

On Tue, Nov 19, 2013 at 7:48 PM, fatemeh ramezani <fr_...@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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