AMBER Archive (2007)

Subject: Re: AMBER: RED-vIII fails

From: Jesper Soerensen (lists_at_jsx.dk)
Date: Tue Oct 30 2007 - 03:16:36 CST


Files are attached, I figured I'd include all the data, as the file size
wasn't too different.

Thanks,
Jesper

On Mon, 2007-10-29 at 17:25 +0100, FyD wrote:
> Quoting Jesper Soerensen <lists_at_jsx.dk>:
>
> > I am trying to prepare parameters for a neutral C-terminal amino acid. I
> > have done as in the tutorial, but the program fails giving the following
> > message:
> >
> >> The RESP-A1 charges are being derived for ALL molecules...
> >> [ FAILED ]
> >> See the "output(1|2)_mm" file
> >
> > If I look at the output of "output2_mm" then at the end of the file it
> > says:
> >> Unit 3 Error on OPEN: qout1_mm
>
> Could you provide the end of the output1_mm and output2_mm files ?
> Let's say the last 100 lines...
>
> > And I have checked there is no file by that name. Have I done something
> > wrong? I have run all the QM (g03) calculations in RED, but I have
> > checked and made sure that they have all returned an optimized
> > structure. I have included the headers of the two files I am using.
>
> regards, Francois
>
>
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 -----------------------------------------------
      Restrained ESP Fit 2.3 Amber 4.1
 -----------------------------------------------
  RESP-A1 project. RESP input generated by R.E.D.
 -----------------------------------------------

 inopt = 0 ioutopt = 1
 nmol = 9 iqopt = 1
 ihfree = 1 irstrnt = 1
 iunits = 0 qwt = 0.00050000

 %RESP-I-MULT_MOL, multiple-molecule run of 9 molecules

 Reading input for molecule 1 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
    1 6 0
    2 1 0
    3 1 0
    4 1 0
    5 6 0
    6 8 0
    7 7 0
    8 1 0
    9 6 0
   10 1 0
   11 6 0
   12 1 0
   13 8 0
   14 1 0
   15 6 0
   16 1 0
   17 1 0
   18 1 0
   19 6 0
   20 8 0
   21 7 0
   22 1 0
   23 6 0
   24 1 0
   25 1 0
   26 1 0

 Reading input for molecule 2 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
   27 6 0
   28 1 0
   29 1 0
   30 1 0
   31 6 0
   32 8 0
   33 7 0
   34 1 0
   35 6 0
   36 1 0
   37 6 0
   38 1 0
   39 8 0
   40 1 0
   41 6 0
   42 1 0
   43 1 0
   44 1 0
   45 6 0
   46 8 0
   47 7 0
   48 1 0
   49 6 0
   50 1 0
   51 1 0
   52 1 0

 Reading input for molecule 3 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
   53 6 0
   54 1 0
   55 1 0
   56 1 0
   57 6 0
   58 8 0
   59 7 0
   60 1 0
   61 6 0
   62 1 0
   63 6 0
   64 1 0
   65 8 0
   66 1 0
   67 6 0
   68 1 0
   69 1 0
   70 1 0
   71 6 0
   72 8 0
   73 7 0
   74 1 0
   75 6 0
   76 1 0
   77 1 0
   78 1 0

 Reading input for molecule 4 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
   79 6 0
   80 1 0
   81 1 0
   82 1 0
   83 6 0
   84 8 0
   85 7 0
   86 1 0
   87 6 0
   88 1 0
   89 6 0
   90 1 0
   91 8 0
   92 1 0
   93 6 0
   94 1 0
   95 1 0
   96 1 0
   97 6 0
   98 8 0
   99 7 0
  100 1 0
  101 6 0
  102 1 0
  103 1 0
  104 1 0

 Reading input for molecule 5 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  105 6 0
  106 1 0
  107 1 0
  108 1 0
  109 6 0
  110 8 0
  111 7 0
  112 1 0
  113 6 0
  114 1 0
  115 6 0
  116 1 0
  117 8 0
  118 1 0
  119 6 0
  120 1 0
  121 1 0
  122 1 0
  123 6 0
  124 8 0
  125 7 0
  126 1 0
  127 6 0
  128 1 0
  129 1 0
  130 1 0

 Reading input for molecule 6 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  131 6 0
  132 1 0
  133 1 0
  134 1 0
  135 6 0
  136 8 0
  137 7 0
  138 1 0
  139 6 0
  140 1 0
  141 6 0
  142 1 0
  143 8 0
  144 1 0
  145 6 0
  146 1 0
  147 1 0
  148 1 0
  149 6 0
  150 8 0
  151 7 0
  152 1 0
  153 6 0
  154 1 0
  155 1 0
  156 1 0

 Reading input for molecule 7 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  157 6 0
  158 1 0
  159 1 0
  160 1 0
  161 6 0
  162 8 0
  163 7 0
  164 1 0
  165 6 0
  166 1 0
  167 6 0
  168 1 0
  169 8 0
  170 1 0
  171 6 0
  172 1 0
  173 1 0
  174 1 0
  175 6 0
  176 8 0
  177 7 0
  178 1 0
  179 6 0
  180 1 0
  181 1 0
  182 1 0

 Reading input for molecule 8 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  183 6 0
  184 1 0
  185 1 0
  186 1 0
  187 6 0
  188 8 0
  189 7 0
  190 1 0
  191 6 0
  192 1 0
  193 6 0
  194 1 0
  195 8 0
  196 1 0
  197 6 0
  198 1 0
  199 1 0
  200 1 0
  201 6 0
  202 8 0
  203 7 0
  204 1 0
  205 6 0
  206 1 0
  207 1 0
  208 1 0

 Reading input for molecule 9 weight: 1.000
 Acetic

 Total charge (ich): 0
 Number of centers: 8
  209 6 0
  210 1 0
  211 1 0
  212 1 0
  213 6 0
  214 8 0
  215 8 0
  216 1 0
    1 1 1 2 1 3 1 4 1 5 1 6


 -----------------------------------------------
      Restrained ESP Fit 2.3 Amber 4.1
 -----------------------------------------------
  RESP-A1 project. RESP input generated by R.E.D.
 -----------------------------------------------

 inopt = 0 ioutopt = 1
 nmol = 9 iqopt = 2
 ihfree = 1 irstrnt = 1
 iunits = 0 qwt = 0.00100000

 %RESP-I-MULT_MOL, multiple-molecule run of 9 molecules

 Reading input for molecule 1 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
    1 6 -1
    2 1 -1
    3 1 -1
    4 1 -1
    5 6 -1
    6 8 -1
    7 7 -1
    8 1 -1
    9 6 -1
   10 1 -1
   11 6 -1
   12 1 -1
   13 8 -1
   14 1 -1
   15 6 0
   16 1 0
   17 1 16
   18 1 16
   19 6 -1
   20 8 -1
   21 7 -1
   22 1 -1
   23 6 -1
   24 1 -1
   25 1 -1
   26 1 -1

 Reading input for molecule 2 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
   27 6 -1
   28 1 -1
   29 1 -1
   30 1 -1
   31 6 -1
   32 8 -1
   33 7 -1
   34 1 -1
   35 6 -1
   36 1 -1
   37 6 -1
   38 1 -1
   39 8 -1
   40 1 -1
   41 6 0
   42 1 0
   43 1 16
   44 1 16
   45 6 -1
   46 8 -1
   47 7 -1
   48 1 -1
   49 6 -1
   50 1 -1
   51 1 -1
   52 1 -1

 Reading input for molecule 3 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
   53 6 -1
   54 1 -1
   55 1 -1
   56 1 -1
   57 6 -1
   58 8 -1
   59 7 -1
   60 1 -1
   61 6 -1
   62 1 -1
   63 6 -1
   64 1 -1
   65 8 -1
   66 1 -1
   67 6 0
   68 1 0
   69 1 16
   70 1 16
   71 6 -1
   72 8 -1
   73 7 -1
   74 1 -1
   75 6 -1
   76 1 -1
   77 1 -1
   78 1 -1

 Reading input for molecule 4 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
   79 6 -1
   80 1 -1
   81 1 -1
   82 1 -1
   83 6 -1
   84 8 -1
   85 7 -1
   86 1 -1
   87 6 -1
   88 1 -1
   89 6 -1
   90 1 -1
   91 8 -1
   92 1 -1
   93 6 0
   94 1 0
   95 1 16
   96 1 16
   97 6 -1
   98 8 -1
   99 7 -1
  100 1 -1
  101 6 -1
  102 1 -1
  103 1 -1
  104 1 -1

 Reading input for molecule 5 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  105 6 -1
  106 1 -1
  107 1 -1
  108 1 -1
  109 6 -1
  110 8 -1
  111 7 -1
  112 1 -1
  113 6 -1
  114 1 -1
  115 6 -1
  116 1 -1
  117 8 -1
  118 1 -1
  119 6 0
  120 1 0
  121 1 16
  122 1 16
  123 6 -1
  124 8 -1
  125 7 -1
  126 1 -1
  127 6 -1
  128 1 -1
  129 1 -1
  130 1 -1

 Reading input for molecule 6 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  131 6 -1
  132 1 -1
  133 1 -1
  134 1 -1
  135 6 -1
  136 8 -1
  137 7 -1
  138 1 -1
  139 6 -1
  140 1 -1
  141 6 -1
  142 1 -1
  143 8 -1
  144 1 -1
  145 6 0
  146 1 0
  147 1 16
  148 1 16
  149 6 -1
  150 8 -1
  151 7 -1
  152 1 -1
  153 6 -1
  154 1 -1
  155 1 -1
  156 1 -1

 Reading input for molecule 7 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  157 6 -1
  158 1 -1
  159 1 -1
  160 1 -1
  161 6 -1
  162 8 -1
  163 7 -1
  164 1 -1
  165 6 -1
  166 1 -1
  167 6 -1
  168 1 -1
  169 8 -1
  170 1 -1
  171 6 0
  172 1 0
  173 1 16
  174 1 16
  175 6 -1
  176 8 -1
  177 7 -1
  178 1 -1
  179 6 -1
  180 1 -1
  181 1 -1
  182 1 -1

 Reading input for molecule 8 weight: 1.000
 Threonine-dipeptide,

 Total charge (ich): 0
 Number of centers: 26
  183 6 -1
  184 1 -1
  185 1 -1
  186 1 -1
  187 6 -1
  188 8 -1
  189 7 -1
  190 1 -1
  191 6 -1
  192 1 -1
  193 6 -1
  194 1 -1
  195 8 -1
  196 1 -1
  197 6 0
  198 1 0
  199 1 16
  200 1 16
  201 6 -1
  202 8 -1
  203 7 -1
  204 1 -1
  205 6 -1
  206 1 -1
  207 1 -1
  208 1 -1

 Reading input for molecule 9 weight: 1.000
 Acetic

 Total charge (ich): 0
 Number of centers: 8
  209 6 -1
  210 1 -1
  211 1 -1
  212 1 -1
  213 6 -1
  214 8 -1
  215 8 -1
  216 1 -1

  Unit 3 Error on OPEN: qout1_mm

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