[gmx-users] how modify the forcefield amino acid definitions for non-naturally occuring amino acids?

Kirill Bessonov kbessonov at gmail.com
Sun Mar 4 22:36:51 CET 2012

Dear Gmx users,

I had been using Gromacs for couple of years and always found these forums
quite helpful. Right now again I have another question to ask that I was
not able to figure out yet myself and reading previous posts.

I need to the ffG53a6 forcefield to be able to recognize the non-standard
amino acid like AZE (Azetidine-2-carboxylic acid) which closely resembles
Proline, but lacks CH2 group in the ring of the side-group, making the
R-group a 4 member ring instead of 5. Thus, this amino acid has very close
chemical structure to the Proline which is properly defined in the *.rtp
file as below

[ PRO ]
 [ atoms ]
    N     N     0.00000     0
   CA   CH1     0.00000     1
   CB  CH2R     0.00000     1
   CG  CH2R     0.00000     2
   CD  CH2R     0.00000     2
    C     C       0.450     3
    O     O      -0.450     3
 [ bonds ]
    N    CA    gb_21
    N    CD    gb_21
   CA    CB    gb_27
   CA     C    gb_27
   CB    CG    gb_27
   CG    CD    gb_27
    C     O    gb_5
    C    +N    gb_10
 [ angles ]
;  ai    aj    ak   gromos type
   -C     N    CA     ga_31
   -C     N    CD     ga_31
   CA     N    CD     ga_21
    N    CA    CB     ga_13
    N    CA     C     ga_13
   CB    CA     C     ga_13
   CA    CB    CG     ga_13
   CB    CG    CD     ga_13
    N    CD    CG     ga_13
   CA     C     O     ga_30
   CA     C    +N     ga_19
    O     C    +N     ga_33
 [ impropers ]
;  ai    aj    ak    al   gromos type
    N    -C    CA    CD     gi_1
   CA     N     C    CB     gi_2
    C    CA    +N     O     gi_1
 [ dihedrals ]
;  ai    aj    ak    al   gromos type
  -CA    -C     N    CA     gd_14
   -C     N    CA     C     gd_39
   CA     N    CD    CG     gd_39
    N    CA    CB    CG     gd_34
    N    CA     C    +N     gd_40
   CA    CB    CG    CD     gd_34
   CB    CG    CD     N     gd_34

The question is how can I derive from this Proline definition topology the
corresponding topology for AZE? The problem is that I do know how to
interpret the each column such as the "gromos definition" column gd_14,
etc, as well as other columns..... Where can I get information or tutorials
about this important issue on how to create own topology files? Maybe
someone can explain those columns in easy terms? What are corresponding
atoms referred by atom names in the final structure as the there is not
ASCI diagram of those as I've seen in AMBER tutorials?

Also I am interested in knowing on how the topology files are created from

Any help will be greatly appreciated.

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