[gmx-users] Acetylation of lysine

[Justin Lemkul]

On 1/22/18 9:58 PM, Shraddha Parate wrote:
> 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?

Probably a consequence of not defining the residue as Protein in 
residuetypes.dat.

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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