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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