[gmx-users] Add new residue to forcefield

fatemeh ramezani fr_750 at yahoo.com
Tue Dec 16 10:58:39 CET 2014


Hi Dear gmx-users
I want to simulate a tripeptide contain hydroxyprolin 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       HO      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
    HO    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    HO
    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:

[ bondtypes ]
CG   OH   2    0.144   6100000.0     ;
OH   HO  2    0.100  15700000.0     ;


[ 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     HO      2   109.5      450.0

[ dihedraltypes ]
CG   CB   CD   OH     1    35.3  334.8
CB   CG   OH   HO    1      0.0    1.3 3


 After pdb2gmx command top file was generated:
...
; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue  22 PRO rtp PRO  q +0.9
     1   opls_309     22    PRO      N      1       -0.2    14.0067   ; qtot -0.2
     2   opls_310     22    PRO     H1      1       0.31      1.008   ; qtot 0.11
     3   opls_310     22    PRO     H2      1       0.31      1.008   ; qtot 0.42
     4   opls_246     22    PRO     CA      1       0.13     12.011   ; qtot 0.55
     5   opls_140     22    PRO     HA      1       0.06      1.008   ; qtot 0.61
     6   opls_136     22    PRO     CB      2      -0.12     12.011   ; qtot 0.49
     7   opls_140     22    PRO    HB1      2       0.06      1.008   ; qtot 0.55
     8   opls_140     22    PRO    HB2      2       0.06      1.008   ; qtot 0.61
     9   opls_136     22    PRO     CG      3      -0.12     12.011   ; qtot 0.49
    10   opls_140     22    PRO    HG1      3       0.06      1.008   ; qtot 0.55
    11   opls_140     22    PRO    HG2      3       0.06      1.008   ; qtot 0.61
    12   opls_296     22    PRO     CD      4       0.17     12.011   ; qtot 0.78
    13   opls_140     22    PRO    HD1      4       0.06      1.008   ; qtot 0.84
    14   opls_140     22    PRO    HD2      4       0.06      1.008   ; qtot 0.9
    15   opls_235     22    PRO      C      5        0.5     12.011   ; qtot 1.4
    16   opls_236     22    PRO      O      5       -0.5    15.9994   ; qtot 0.9
; residue  23 HYP rtp HYP  q -0.4
    17   opls_239     23    HYP      N      6      -0.14    14.0067   ; qtot 0.76
    18   opls_246     23    HYP     CA      6       0.01     12.011   ; qtot 0.77
    19   opls_140     23    HYP     HA      6       0.06      1.008   ; qtot 0.83
    20   opls_136     23    HYP     CB      7      -0.12     12.011   ; qtot 0.71
    21   opls_140     23    HYP    HB1      7       0.06      1.008   ; qtot 0.77
    22   opls_140     23    HYP    HB2      7       0.06      1.008   ; qtot 0.83
    23   opls_136     23    HYP     CG      8      -0.12     12.011   ; qtot 0.71
    24   opls_140     23    HYP     HG      8       0.06      1.008   ; qtot 0.77
    25   opls_167     23    HYP     OH      8     -0.683    15.9994   ; qtot 0.087
    26   opls_168     23    HYP     HO      8      0.435      1.008   ; qtot 0.522
    27   opls_245     23    HYP     CD      9      -0.05     12.011   ; qtot 0.472
    28   opls_140     23    HYP     HD      9       0.06      1.008   ; qtot 0.532
    29   opls_235     23    HYP      C     10        0.5     12.011   ; qtot 1.032
    30   opls_236     23    HYP      O     10       -0.5    15.9994   ; qtot 0.532
; residue  24 GLY rtp GLY  q -0.9
    31   opls_238     24    GLY      N     11       -0.5    14.0067   ; qtot 0.032
    32   opls_241     24    GLY      H     11        0.3      1.008   ; qtot 0.332
    33   opls_298     24    GLY     CA     11       0.09     12.011   ; qtot 0.422
    34   opls_140     24    GLY    HA1     11       0.06      1.008   ; qtot 0.482
    35   opls_140     24    GLY    HA2     11       0.06      1.008   ; qtot 0.542
    36   opls_271     24    GLY      C     12        0.7     12.011   ; qtot 1.242
    37   opls_272     24    GLY     O1     12       -0.8    15.9994   ; qtot 0.442
    38   opls_272     24    GLY     O2     12       -0.8    15.9994   ; qtot -0.358
.
.
.
When I grompp, I get this error :
ERROR 1 [file topol.top, line 258]:
  No default Angle types

In topol.top line 258 contain atoms 25  23 27 that are atoms OH  CG  CD and I added the angle between them in [angletypes] section in ffbonded.itp file.

I would be grateful if anyone could shed some light on the origin of 
this error, and on what I can do to correct it.
  Fatemeh Ramezani


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