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

[Hu Zhongqiao]

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). 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?
 
Thanks in advance,
 
 
Zhongqiao Hu
 
Department of Chemical and Biomolecular Engineering
National University of Singapore
117576, Singapore
 
 
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