[gmx-users] Acetylation of lysine

[Shraddha Parate]

Dear Gromacs Users,

I need to perform acetylation of lysine residues in my work for which I
have acetylated the lysine (KAC) from Vienna PTM server. I came across a
paper titled 'A Systematic Framework for Molecular Dynamics Simulations of
Protein Post-Translational Modifications' in which they have reported the
force field parameters for Acetylation of lysine residue. Accordingly, I
made the following changes in aminoacids.rtp file and in aminoacids.hdb
file:

; aminoacids.rtp file (backbone and side chain parameters)

; N6-acetyllysine
[ KAC ]
 [ 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     N    -0.28000     4 ; from the peptide bond
   HZ     H     0.28000     4 ; from the peptide bond
   CH     C     0.28000     5 ; by analogy to the aldehyde group
reported by Dolenc et al. DOI: 10.1093/nar/gki195
  OI2     O    -0.38000     5 ; from the carbonyl group (of e.g. GLN)
  CI1   CH3     0.10000     5 ; by analogy to the aldehyde group
reported by Dolenc et al. DOI: 10.1093/nar/gki195
    C     C       0.380     6
    O     O      -0.380     6
 [ 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    HZ    gb_2
   NZ    CH    gb_9
   CH   OI2    gb_4
   CH   CI1    gb_26
 [ 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    HZ     ga_17
   HZ    NZ    CH     ga_31
   CE    NZ    CH     ga_30
   NZ    CH   OI2     ga_32
   NZ    CH   CI1     ga_18
  OI2    CH   CI1     ga_29
 [ 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
   NZ    CH    CE    HZ     gi_1
   CH   CI1    NZ   OI2     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    CE     gd_17
   CG    CD    CE    NZ     gd_17
   CD    CE    NZ    CH     gd_19
   CE    NZ    CH   CI1     gd_4




; aminoacids.hdb file (hydrogen databese)

; N6-acetyllysine
KAC    2
1	1	H	N	-C	CA
1	1	HZ	NZ	CE	CH


I got the following error:

WARNING: atom H is missing in residue KAC 31 in the pdb file
         You might need to add atom H to the hydrogen database of b
         uilding block KAC
         in the file aminoacids.hdb (see the manual)


WARNING: atom HZ is missing in residue KAC 31 in the pdb file
         You might need to add atom HZ to the hydrogen database of
         building block KAC
         in the file aminoacids.hdb (see the manual)


WARNING: atom H is missing in residue KAC 32 in the pdb file
         You might need to add atom H to the hydrogen database of b
         uilding block KAC
         in the file aminoacids.hdb (see the manual)


WARNING: atom HZ is missing in residue KAC 32 in the pdb file
         You might need to add atom HZ to the hydrogen database of
         building block KAC
         in the file aminoacids.hdb (see the manual)


WARNING: atom H is missing in residue KAC 33 in the pdb file
         You might need to add atom H to the hydrogen database of b
         uilding block KAC
         in the file aminoacids.hdb (see the manual)


WARNING: atom HZ is missing in residue KAC 33 in the pdb file
         You might need to add atom HZ to the hydrogen database of
         building block KAC
         in the file aminoacids.hdb (see the manual)


Can anyone help me in troubleshooting this error?

Regards,
Shraddha M. Parate