[gmx-users] question

[Andrew Bostick]

Dear Justin

Based on your answer (You don't want to be adding 2 HZ here, just one
since it is a peptide bond.), I modified LYS2 in aminoacids.hdb file

LYS2     2
1 1 H N -C CA
1 4 HZ NZ CE CD

But, after pdb2gmx, I encountered with

WARNING: atom HZ1 is missing in residue LYS 540 in the pdb file
         You might need to add atom HZ1 to the hydrogen database of
building block LYS2
         in the file aminoacids.hdb (see the manual)


WARNING: atom HZ2 is missing in residue LYS 540 in the pdb file
         You might need to add atom HZ2 to the hydrogen database of
building block LYS2
         in the file aminoacids.hdb (see the manual).

What is the reason of this issue? Is there problem in my rtp file (about
LYS2 and GLU2 entries)?

[ 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       0.380     2
  OE1    OM      -0.380     2
  OE2    OM     0.00000     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
   CD   OE2    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
   CG    CD   OE2     ga_21
  OE1    CD   OE2     ga_37
 [ 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
   CD   OE1   OE2    CG     gi_1
 [ 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   OE2     gd_2

[ 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     2
   NZ    NT    -0.28000     3
  HZ1     H     0.28000     3
  HZ2     H     0.00000     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
   NZ   HZ2    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
   CE    NZ   HZ2     ga_10
  HZ1    NZ   HZ2     ga_9
 [ 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

Thanks in advance.