[gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??

[Joseph Schwartz]

I was wondering why the Hydrogens from the non N-terminus NH2 group in the uncharged Lysine molecule had charges of 0.36 as specified by gromacs(H1 and H2) when the Jorgensen published value for H's in RCH2NH2 was 0.35.  All of the other charges in this molecule I have found in publications except for those.  The overall charge of the molecule is 0.02 and if the H's were changed to 0.35 it would make the overall molecule uncharged.  Would this alteration be valid?

This is part of the topol.top file.


[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1   opls_900      1   LYSH      N      1       -0.9    14.0067   ; qtot -0.9
     2   opls_909      1   LYSH     H1      1       0.36      1.008   ; qtot -0.54
     3   opls_909      1   LYSH     H2      1       0.36      1.008   ; qtot -0.18
     4   opls_283      1   LYSH     CA      1       0.04     12.011   ; qtot -0.14
     5   opls_140      1   LYSH     HA      1       0.06      1.008   ; qtot -0.08
     6   opls_136      1   LYSH     CB      2      -0.12     12.011   ; qtot -0.2
     7   opls_140      1   LYSH    HB1      2       0.06      1.008   ; qtot -0.14
     8   opls_140      1   LYSH    HB2      2       0.06      1.008   ; qtot -0.08
     9   opls_136      1   LYSH     CG      3      -0.12     12.011   ; qtot -0.2
    10   opls_140      1   LYSH    HG1      3       0.06      1.008   ; qtot -0.14
    11   opls_140      1   LYSH    HG2      3       0.06      1.008   ; qtot -0.08
    12   opls_136      1   LYSH     CD      4      -0.12     12.011   ; qtot -0.2
    13   opls_140      1   LYSH    HD1      4       0.06      1.008   ; qtot -0.14
    14   opls_140      1   LYSH    HD2      4       0.06      1.008   ; qtot -0.08
    15   opls_292      1   LYSH     CE      5       0.19     12.011   ; qtot 0.11
    16   opls_140      1   LYSH    HE1      5       0.06      1.008   ; qtot 0.17
    17   opls_140      1   LYSH    HE2      5       0.06      1.008   ; qtot 0.23
    18   opls_287      1   LYSH     NZ      6       -0.3    14.0067   ; qtot -0.07
    19   opls_290      1   LYSH    HZ1      6       0.33      1.008   ; qtot 0.26
    20   opls_290      1   LYSH    HZ2      6       0.33      1.008   ; qtot 0.59
    21   opls_290      1   LYSH    HZ3      6       0.33      1.008   ; qtot 0.92
    22   opls_271      1   LYSH      C      7        0.7     12.011   ; qtot 1.62
    23   opls_272      1   LYSH     O1      7       -0.8    15.9994   ; qtot 0.82
    24   opls_272      1   LYSH     O2      7       -0.8    15.9994   ; qtot 0.02





      
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