[gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??
Joseph Schwartz
joedogt2 at yahoo.com
Mon Jun 30 20:16:00 CEST 2008
This is a link to a table for the OPLS parameters showing the 0.35 for the Hydrogens in the RNH2 group (not RCH2NH2--my mistake). It is Table 2 on page 64. Again, my question is why Gromacs uses 0.36 for the hydrogens in the non n-terminus NH2 group of the uncharged lysine molecule when the published value shows 0.35??
zarbi.chem.yale.edu/doc/boss46.pdf
--- On Sat, 6/28/08, Joseph Schwartz <joedogt2 at yahoo.com> wrote:
From: Joseph Schwartz <joedogt2 at yahoo.com>
Subject: [gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??
To: gmx-users at gromacs.org
Date: Saturday, June 28, 2008, 11:36 AM
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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--- On Sat, 6/28/08, Joseph Schwartz <joedogt2 at yahoo.com> wrote:
From: Joseph Schwartz <joedogt2 at yahoo.com>
Subject: [gmx-users] Uncharged Lysine Charges on Hydrogens from NH2 group 0.36??
To: gmx-users at gromacs.org
Date: Saturday, June 28, 2008, 11:36 AM
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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