AMBER Archive (2006)

Subject: Re: AMBER: How to develop charge for my deprotonated glycine

From: Jianzhong Liu (zhong_at_udel.edu)
Date: Sat Mar 04 2006 - 21:05:12 CST

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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