Dear Francois,
Thank you very much for your reply. I am a new user to develop charge. It
seems give me some sense about how to develop charge by following your
links. But I still have two questions and hope can get your reply.
I tried to develop central Alanine and NH3(+)-alanine by using RED II with
your methods to get some practices at first. It easily to understand how to
develop central part amino acid by following your links. Here are punch2
file got from ACE-ALA-NME and MeNH3 respectively.
This one is for ACE-ALA-NME (3 different conformations, 2 orientations)
Point charges before & after optimization
NO At.No. q0 q(opt) IVARY d(rstr)/dq
1 6 -0.399767 -0.340289 0 0.002819
2 1 0.095385 0.101815 0 0.000000
3 1 0.130434 0.101815 2 0.000000
4 1 0.130453 0.101815 2 0.000000
5 6 0.668813 0.668813 -1 0.001479
6 8 -0.582506 -0.582506 -1 0.001692
7 7 -0.549906 -0.549906 -1 0.001789
8 6 0.101663 0.101663 -1 0.007013
9 1 0.324106 0.324106 -1 0.000000
10 1 0.049460 0.049460 -1 0.000000
11 6 0.569639 0.569639 -1 0.001729
12 8 -0.566456 -0.566456 -1 0.001738
13 6 -0.098371 -0.155835 0 0.005401
14 1 0.044167 0.057488 0 0.000000
15 1 0.050524 0.057488 14 0.000000
16 1 0.029423 0.057488 14 0.000000
17 7 -0.436566 -0.436566 -1 0.002233
18 6 -0.165890 -0.162526 0 0.005239
19 1 0.305448 0.305448 -1 0.000000
20 1 0.101864 0.099016 0 0.000000
21 1 0.101180 0.099016 20 0.000000
22 1 0.096902 0.099016 20 0.000000
23 6 -0.399767 -0.340289 1 0.002819
24 1 0.095385 0.101815 2 0.000000
25 1 0.130434 0.101815 2 0.000000
26 1 0.130453 0.101815 2 0.000000
27 6 0.668813 0.668813 -1 0.001479
28 8 -0.582506 -0.582506 -1 0.001692
29 7 -0.549906 -0.549906 -1 0.001789
30 6 0.101663 0.101663 -1 0.007013
31 1 0.324106 0.324106 -1 0.000000
32 1 0.049460 0.049460 -1 0.000000
33 6 0.569639 0.569639 -1 0.001729
34 8 -0.566456 -0.566456 -1 0.001738
35 6 -0.098371 -0.155835 13 0.005401
36 1 0.044167 0.057488 14 0.000000
37 1 0.050524 0.057488 14 0.000000
38 1 0.029423 0.057488 14 0.000000
39 7 -0.436566 -0.436566 -1 0.002233
40 6 -0.165890 -0.162526 18 0.005239
41 1 0.305448 0.305448 -1 0.000000
42 1 0.101864 0.099016 20 0.000000
43 1 0.101180 0.099016 20 0.000000
44 1 0.096902 0.099016 20 0.000000
45 6 -0.399767 -0.340289 1 0.002819
46 1 0.095385 0.101815 2 0.000000
47 1 0.130434 0.101815 2 0.000000
48 1 0.130453 0.101815 2 0.000000
49 6 0.668813 0.668813 -1 0.001479
50 8 -0.582506 -0.582506 -1 0.001692
51 7 -0.549906 -0.549906 -1 0.001789
52 6 0.101663 0.101663 -1 0.007013
53 1 0.324106 0.324106 -1 0.000000
54 1 0.049460 0.049460 -1 0.000000
55 6 0.569639 0.569639 -1 0.001729
56 8 -0.566456 -0.566456 -1 0.001738
57 6 -0.098371 -0.155835 13 0.005401
58 1 0.044167 0.057488 14 0.000000
59 1 0.050524 0.057488 14 0.000000
60 1 0.029423 0.057488 14 0.000000
61 7 -0.436566 -0.436566 -1 0.002233
62 6 -0.165890 -0.162526 18 0.005239
63 1 0.305448 0.305448 -1 0.000000
64 1 0.101864 0.099016 20 0.000000
65 1 0.101180 0.099016 20 0.000000
66 1 0.096902 0.099016 20 0.000000
67 6 -0.399767 -0.340289 1 0.002819
68 1 0.095385 0.101815 2 0.000000
69 1 0.130434 0.101815 2 0.000000
70 1 0.130453 0.101815 2 0.000000
71 6 0.668813 0.668813 -1 0.001479
72 8 -0.582506 -0.582506 -1 0.001692
73 7 -0.549906 -0.549906 -1 0.001789
74 6 0.101663 0.101663 -1 0.007013
75 1 0.324106 0.324106 -1 0.000000
76 1 0.049460 0.049460 -1 0.000000
77 6 0.569639 0.569639 -1 0.001729
78 8 -0.566456 -0.566456 -1 0.001738
79 6 -0.098371 -0.155835 13 0.005401
80 1 0.044167 0.057488 14 0.000000
81 1 0.050524 0.057488 14 0.000000
82 1 0.029423 0.057488 14 0.000000
83 7 -0.436566 -0.436566 -1 0.002233
84 6 -0.165890 -0.162526 18 0.005239
85 1 0.305448 0.305448 -1 0.000000
86 1 0.101864 0.099016 20 0.000000
87 1 0.101180 0.099016 20 0.000000
88 1 0.096902 0.099016 20 0.000000
89 6 -0.399767 -0.340289 1 0.002819
90 1 0.095385 0.101815 2 0.000000
91 1 0.130434 0.101815 2 0.000000
92 1 0.130453 0.101815 2 0.000000
93 6 0.668813 0.668813 -1 0.001479
94 8 -0.582506 -0.582506 -1 0.001692
95 7 -0.549906 -0.549906 -1 0.001789
96 6 0.101663 0.101663 -1 0.007013
97 1 0.324106 0.324106 -1 0.000000
98 1 0.049460 0.049460 -1 0.000000
99 6 0.569639 0.569639 -1 0.001729
100 8 -0.566456 -0.566456 -1 0.001738
101 6 -0.098371 -0.155835 13 0.005401
102 1 0.044167 0.057488 14 0.000000
103 1 0.050524 0.057488 14 0.000000
104 1 0.029423 0.057488 14 0.000000
105 7 -0.436566 -0.436566 -1 0.002233
106 6 -0.165890 -0.162526 18 0.005239
107 1 0.305448 0.305448 -1 0.000000
108 1 0.101864 0.099016 20 0.000000
109 1 0.101180 0.099016 20 0.000000
110 1 0.096902 0.099016 20 0.000000
111 6 -0.399767 -0.340289 1 0.002819
112 1 0.095385 0.101815 2 0.000000
113 1 0.130434 0.101815 2 0.000000
114 1 0.130453 0.101815 2 0.000000
115 6 0.668813 0.668813 -1 0.001479
116 8 -0.582506 -0.582506 -1 0.001692
117 7 -0.549906 -0.549906 -1 0.001789
118 6 0.101663 0.101663 -1 0.007013
119 1 0.324106 0.324106 -1 0.000000
120 1 0.049460 0.049460 -1 0.000000
121 6 0.569639 0.569639 -1 0.001729
122 8 -0.566456 -0.566456 -1 0.001738
123 6 -0.098371 -0.155835 13 0.005401
124 1 0.044167 0.057488 14 0.000000
125 1 0.050524 0.057488 14 0.000000
126 1 0.029423 0.057488 14 0.000000
127 7 -0.436566 -0.436566 -1 0.002233
128 6 -0.165890 -0.162526 18 0.005239
129 1 0.305448 0.305448 -1 0.000000
130 1 0.101864 0.099016 20 0.000000
131 1 0.101180 0.099016 20 0.000000
132 1 0.096902 0.099016 20 0.000000
It seems I got same charges for different conformation and orientations. So
I just choose following charge for my alanine. Is that correct?
7 7 -0.549906 -0.549906 -1 0.001789
8 6 0.101663 0.101663 -1 0.007013
9 1 0.324106 0.324106 -1 0.000000
10 1 0.049460 0.049460 -1 0.000000
11 6 0.569639 0.569639 -1 0.001729
12 8 -0.566456 -0.566456 -1 0.001738
13 6 -0.098371 -0.155835 0 0.005401
14 1 0.044167 0.057488 0 0.000000
15 1 0.050524 0.057488 14 0.000000
16 1 0.029423 0.057488 14 0.000000
Also, I tried to develop NH3(+)-alanine by using following
This one is for MeNH3 (just 2 orientations).
Point charges before & after optimization
NO At.No. q0 q(opt) IVARY d(rstr)/dq
1 6 -0.046344 -0.046344 -1 0.009073
2 1 0.118249 0.118249 -1 0.000000
3 1 0.118249 0.118249 -1 0.000000
4 1 0.118249 0.118249 -1 0.000000
5 7 -0.218180 -0.218180 -1 0.004167
6 1 0.303290 0.303290 -1 0.000000
7 1 0.303200 0.303200 -1 0.000000
8 1 0.303288 0.303288 -1 0.000000
9 6 -0.046344 -0.046344 -1 0.009073
10 1 0.118249 0.118249 -1 0.000000
11 1 0.118249 0.118249 -1 0.000000
12 1 0.118249 0.118249 -1 0.000000
13 7 -0.218180 -0.218180 -1 0.004167
14 1 0.303290 0.303290 -1 0.000000
15 1 0.303200 0.303200 -1 0.000000
16 1 0.303288 0.303288 -1 0.000000
I got same charge for these two orientations.
Your links
http://www.u-picardie.fr/labo/lbpd/REDDB/uploadfile/F-7/info.html
gives two PDB files about Methylammonium and
N-Acetyl-dimethylalanine-N'-methylamide to develop (+)NH3-terminal fragment
of dimethylalanine. I am not sure I understand exactly how to develop
(+)NH3-terminal fragment of dimethylalanine by using your two PDB files
My second questions is, how can I combine above results Methylammonium and
ACE-ALA-NME to get NH3(+)-alanine?
Thanks,
Jianzhong Liu
Chemistry & Biochemistry
University of Delaware
Newark, DE 19716
Tel: 302-831-3522(O)
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Received on Sun Mar 05 2006 - 06:10:22 PST
