[gmx-users] Conversion of improper angles from amber object file to gromacs

[Justin Lemkul]

On 3/24/20 3:26 PM, Daniel Bauer wrote:
> Hi,
>
> I  am trying to convert forcefield parameters of zwitterionic glycine
> from an amber object file format to gromacs .rtp (to use it with
> amber99sb, which lacks zwitterionic amino acids).
>
> The amber library file I plan to use can be found here:
> https://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/zaa.off
>
> This is what i have so far:
>
> [ZG]
>   [ atoms ]
>       N    N3          -0.408600     1
>      H1    H            0.300300     2
>      H2    H            0.300300     3
>      H3    H            0.300300     4
>      CA    CT          -0.026400     5
>     HA1    H1           0.073800     6
>     HA2    H1           0.073800     7
>       C    C            0.835500     8
>       O    O2          -0.724500     9
>     OXT    O2          -0.724500    10
>   [ bonds ]
>       N    H1
>       N    H2
>       N    H3
>       N    CA
>      CA   HA1
>      CA   HA2
>      CA     C
>       C     O
>       C    OXT
>
> However, I am unsure about the correct conversion of impropers. In the
> .off file format, those are based on the atom type, while gromacs
> expects them to be based on atom names. This leaves room for some
> ambiguity when the same atom type is used multiple types (i.e the COO or
> NH3 group).
>
> The improper parameter section of the .off file looks like this:
>
> !entry.zaa_improper.parm.torsions table  str type1  str type2  str
> type3  str type4  int type  dbl kp  int n  dbl p0  str desc
>   "CT" "O2" "C" "O2" 1 10.500000 2 3.141594 ""
>   "CT" "N" "C" "O" 1 10.500000 2 3.141594 ""
>
> Now, for the CT-O2-C-O2 improper, this would map to two possible
> combinations:
>
>    [ impropers ]
>    ;  atom1 atom2 atom3 atom4 phase(deg) kd(kJ/mol-1rad-2) dn
>       CA    O    C     OXT    180        43.932            2
>       CA    OXT    C     O    180        43.932            2
>
> Are both entries required in the gromacs [ improper ] section or must I
> put only one of them?

You only need one, otherwise you end up with double the intended 
strength of the improper.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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