[gmx-users] non-intergral charge for L-alanine molecules?

[Mark Abraham]

> I want to simulated transport of D- and L- alanine molecules. First I
> tried using ffg43a1 force field, but D-analine will quickly flip to
> L-alanine during energy minimization (I dont know why).

I guess either you gave it the wrong enantiomer to start with, or your
minimization step was too large and you happened to induce a flip with one
force field and not the other. There's nothing about any force field that
will cause preference for one enantiomer over another.

> Alternatively, I
> tried oplsaa force fields. That's OK without flip from D- to L-. But one
> problem is that when I used
>
> pdb2gmx -f L_alanine.pdb -p L_alanine.top -o L_alanine.gro -ff oplsaa
>
> The produced L_alanine.top showed that L_alanine molecule has
> non-integral charge, which is obvioulsy unrealisitc.
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
>      1   opls_287      1    ALA      N      1       -0.3    14.0067   ;
> qtot -0.3
>      2   opls_290      1    ALA     H1      1       0.33      1.008   ;
> qtot 0.03
>      3   opls_290      1    ALA     H2      1       0.33      1.008   ;
> qtot 0.36
>      4   opls_290      1    ALA     H3      1       0.33      1.008   ;
> qtot 0.69
>      5   opls_283      1    ALA     CA      1       0.04     12.011   ;
> qtot 0.73
>      6   opls_140      1    ALA     HA      1       0.06      1.008   ;
> qtot 0.79
>      7   opls_135      1    ALA     CB      2      -0.18     12.011   ;
> qtot 0.61
>      8   opls_140      1    ALA    HB1      2       0.06      1.008   ;
> qtot 0.67
>      9   opls_140      1    ALA    HB2      2       0.06      1.008   ;
> qtot 0.73
>     10   opls_140      1    ALA    HB3      2       0.06      1.008   ;
> qtot 0.79
>     11   opls_271      1    ALA      C      3        0.7     12.011   ;
> qtot 1.49
>     12   opls_272      1    ALA     O1      3       -0.8    15.9994   ;
> qtot 0.69
>     13   opls_272      1    ALA     O2      3       -0.8    15.9994   ;
> qtot -0.11
>
> I opened ffoplsaa.rtp and find the atom types for ALA residue is
>
> [ ALA ]
>  [ atoms ]
>      N    opls_238   -0.500     1
>      H    opls_241    0.300     1
>     CA    opls_224B   0.140     1
>     HA    opls_140    0.060     1
>     CB    opls_135   -0.180     2
>    HB1    opls_140    0.060     2
>    HB2    opls_140    0.060     2
>    HB3    opls_140    0.060     2
>      C    opls_235    0.500     3
>      O    opls_236   -0.500     3
>
> I found that charges of atoms in L_alanine molecule are different from
> charges of corresponding atoms in ALA residue. I want to ask
>
> (1) why L_alanine molecule has non-integral charge? Is it right?
> (2) why identical atoms in L_alanine and ALA residue have different
> charges?

Would you expect a carbon and oxygen in a mid-chain residue to have the
same partial charge as a carbon and oxygen in a terminal carboxyl group?

You should read chapter five of the manual thoroughly, and in particular
the section about termini databases.

Then, when you use pdb2gmx to try to create a zwitterion, choose the
options that allow you to make one.

Mark