[gmx-users] question

[Andrew Bostick]

Dear Justin

Since I want to consider the special bond between CD atom of GLU residue
form peptide 1 and NZ atom of LYS residue from peptide 2, I did following
steps:

1) I created 1 pdb file containing 2 peptides without any connection
between aformentioned atoms (CD & NZ). I deleted OE2 atom of GLU residue
and HZ2 and HZ3 atoms of LYS residue.

2) I created a new entry in specbond.dat and two .rtp entries in gromos
43a1.ff. These are as follows:

In specbond.dat file:
GLU     CD      1       LYS     NZ      1       0.13    GLU2    LYS2

In aminoacids.rtp file:
[ LYS2 ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG   CH2     0.00000     2
   CD   CH2     0.00000     2
   CE   CH2     0.00000     3
   NZ    NT    -0.50000     3
  HZ1     H     0.50000     3
    C     C       0.380     4
    O     O      -0.380     4
 [ bonds ]
    N     H    gb_2
    N    CA    gb_20
   CA     C    gb_26
    C     O    gb_4
    C    +N    gb_9
   CA    CB    gb_26
   CB    CG    gb_26
   CG    CD    gb_26
   CD    CE    gb_26
   CE    NZ    gb_20
   NZ   HZ1    gb_2
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
    N    CA     C     ga_12
   CA     C    +N     ga_18
   CA     C     O     ga_29
    O     C    +N     ga_32
    N    CA    CB     ga_12
    C    CA    CB     ga_12
   CA    CB    CG     ga_14
   CB    CG    CD     ga_14
   CG    CD    CE     ga_14
   CD    CE    NZ     ga_14
   CE    NZ   HZ1     ga_10
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
    C    CA    +N     O     gi_1
   CA     N     C    CB     gi_2
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4
   -C     N    CA     C     gd_19
    N    CA     C    +N     gd_20
    N    CA    CB    CG     gd_17
   CA    CB    CG    CD     gd_17
   CB    CG    CD    CE     gd_17
   CG    CD    CE    NZ     gd_17
   CD    CE    NZ   HZ1     gd_14
----------------------------------------------

[ GLU2 ]
 [ atoms ]
    N     N    -0.28000     0
    H     H     0.28000     0
   CA   CH1     0.00000     1
   CB   CH2     0.00000     1
   CG   CH2     0.00000     1
   CD     C     0.50000     2
  OE1    OM    -0.50000     2
    C     C       0.380     3
    O     O      -0.380     3
 [ bonds ]
    N     H    gb_2
    N    CA    gb_20
   CA     C    gb_26
    C     O    gb_4
    C    +N    gb_9
   CA    CB    gb_26
   CB    CG    gb_26
   CG    CD    gb_26
   CD   OE1    gb_5
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N     H     ga_31
    H     N    CA     ga_17
   -C     N    CA     ga_30
    N    CA     C     ga_12
   CA     C    +N     ga_18
   CA     C     O     ga_29
    O     C    +N     ga_32
    N    CA    CB     ga_12
    C    CA    CB     ga_12
   CA    CB    CG     ga_14
   CB    CG    CD     ga_14
   CG    CD   OE1     ga_21
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA     H     gi_1
    C    CA    +N     O     gi_1
   CA     N     C    CB     gi_2
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_4
   -C     N    CA     C     gd_19
    N    CA     C    +N     gd_20
    N    CA    CB    CG     gd_17
   CA    CB    CG    CD     gd_17

After using pdb2gmx, I encountered with:

WARNING: atom OE2 is missing in residue Glu 417 in the pdb file.

What is wrong in my steps?

Thanks in advance.