[gmx-users] add a group to an amino acid

[hengame fallah]

Hi,
I'm using the OPLS force field.

[ PHE ]
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
    CA    opls_224B   0.140     1
    HA    opls_140    0.060     1
    CB    opls_149   -0.005     2
   HB1    opls_140    0.060     2
   HB2    opls_140    0.060     2
    CG    opls_145   -0.115     2
   CD1    opls_145   -0.115     3
   HD1    opls_146    0.115     3
   CD2    opls_145   -0.115     4
   HD2    opls_146    0.115     4
   CE1    opls_145   -0.115     5
   HE1    opls_146    0.115     5
   CE2    opls_145   -0.115     6
   HE2    opls_146    0.115     6
    CZ    opls_145   -0.115     7
    HZ    opls_146    0.115     7
     C    opls_235    0.500     8
     O    opls_236   -0.500     8

I want to attach "CL" atom instead of HZ
i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and
top files.
What should i do to get rid of this HZ and attach CL instead.
(I edited top and gro files and remove HZ from them, it seemed to work
properly at first, but when i tried to do energy minimization, it had errors
in top file
 and i realized that it couldn't recognized the bond between CL and CZ):

ERROR 1 [file topol.top, line 150]:
  No default Bond types


ERROR 2 [file topol.top, line 422]:
  No default Angle types


ERROR 3 [file topol.top, line 423]:
  No default Angle types

  *"topol.top":*
...
    58   opls_146      3    PHE     HE2     22      0.115      1.008    ;
qtot 0.9
    59   opls_145      3    PHE     CZ       23     -0.115     12.011   ;
qtot 0.785
    60   opls_271      3    PHE     C         24        0.7     12.011     ;
qtot 1.6
    61   opls_272      3    PHE     O1       24       -0.8    15.9994    ;
qtot 0.8
    62   opls_272      3    PHE     O2       24       -0.8    15.9994    ;
qtot 0
    63   opls_135      4    EtOH    CB       25      -0.18     12.011    ;
qtot -0.18
    64   opls_140      4    EtOH    HB1     25       0.06      1.008     ;
qtot -0.12
    65   opls_140      4    EtOH    HB2     25       0.06      1.008     ;
qtot -0.06
    66   opls_401      5    CL        CL       26         -1     35.453
; qtot -1.06
...
[ bonds ]
...
  59    66     1
   60    61     1
   60    62     1
   63    64     1
   63    65     1
...
[ angles ]
...
   58    57    59     1
   55    59    57     1
   55    59    66     1
   57    59    66     1
   45    60    61     1
   45    60    62     1
   61    60    62     1
   64    63    65     1
...
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