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    On 31/03/2011 6:17 PM, ahmet yıldırım wrote:
    <blockquote
      cite="mid:AANLkTindMsZuT0=59jYN_040V6hS+kavAmvh4E8Mi37C@mail.gmail.com"
      type="cite">Dear Tsjerk,<br>
      <br>
      I will ask you one thing but <span id="result_box"
        class="short_text" lang="en"><span title="Alternatif çevirileri
          görmek için tıklayın" class="hps">please do</span> <span
          title="Alternatif çevirileri görmek için tıklayın" class="hps">not
          get angry (</span></span><span id="result_box"
        class="short_text" lang="en"><span title="Alternatif çevirileri
          görmek için tıklayın" class="hps">I know</span> <span
          title="Alternatif çevirileri görmek için tıklayın" class="hps">you
          are not a</span> <span title="Alternatif çevirileri görmek
          için tıklayın" class="hps">private</span> <span
          title="Alternatif çevirileri görmek için tıklayın" class="hps">tutor</span></span>
      but I need your helps).<br>
      <span id="result_box" class="short_text" lang="en"><span
          title="Alternatif çevirileri görmek için tıklayın" class="hps"><br>
          How do I apply on the files (EDO.itp and TRS.itp) that you
          said? (or can you suggest a tutorial?)<br>
        </span></span></blockquote>
    <br>
    You'll need to become familiar with the file format, so that you
    know what all the columns of data mean, so you know where the charge
    groups are specified. Chapter 5 of the manual is your first port of
    call. If you have read that and still have questions about detail,
    please ask on the list :-)<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:AANLkTindMsZuT0=59jYN_040V6hS+kavAmvh4E8Mi37C@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">2011/3/31 Mark Abraham <span dir="ltr">&lt;<a
            moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span><br>
        <blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
          0.8ex; border-left: 1px solid rgb(204, 204, 204);
          padding-left: 1ex;">
          <div text="#000000" bgcolor="#ffffff">
            <div class="im"> On 31/03/2011 5:18 PM, ahmet yıldırım
              wrote:
              <blockquote type="cite">Dear users,<br>
                <br>
                Before energy minimization step , I performed the
                preprosessing step using grompp .<br>
                However, there are two note that :<br>
                <br>
                <b><u>NOTE 1 [file topol.top, line 52]:</u></b><br>
                  System has non-zero total charge: -1.500000e+01<br>
              </blockquote>
              <br>
            </div>
            This is an integer. See <a moz-do-not-send="true"
              href="http://en.wikipedia.org/wiki/Scientific_notation#E_notation"
              target="_blank">http://en.wikipedia.org/wiki/Scientific_notation#E_notation</a>
            and <a moz-do-not-send="true"
              href="http://www.gromacs.org/Documentation/Floating_Point_Arithmetic"
              target="_blank">http://www.gromacs.org/Documentation/Floating_Point_Arithmetic</a> 
            <br>
            <div class="im"> <br>
              <blockquote type="cite"><u><b>NOTE 2 [file topol.top]:</b></u><br>
                  The largest charge group contains 11 atoms.<br>
                  Since atoms only see each other when the centers of
                geometry of the charge<br>
                  groups they belong to are within the cut-off distance,
                too large charge<br>
                  groups can lead to serious cut-off artifacts.<br>
                  For efficiency and accuracy, charge group should
                consist of a few atoms.<br>
                  For all-atom force fields use: CH3, CH2, CH, NH2, NH,
                OH, CO2, CO, etc.<br>
              </blockquote>
              <br>
            </div>
            See Tsjerk's email.<br>
            <font color="#888888"> <br>
              Mark</font>
            <div>
              <div class="h5"><br>
                <br>
                <blockquote type="cite"><b><br>
                    PS: </b>TRS and EDO are not aminoacid<b><br>
                    <br>
                    <u>TRS.itp:</u></b><br>
                  ..<br>
                  [ moleculetype ]<br>
                  ; Name nrexcl<br>
                  TRS      3<br>
                  <br>
                  [ atoms ]<br>
                  ;   nr      type  resnr resid  atom  cgnr   charge    
                  mass<br>
                       1        OA     1  TRS      O1     1   -0.119 
                  15.9994   <br>
                       2         H     1  TRS     H13     1    0.032  
                  1.0080   <br>
                       3       CH2     1  TRS      C1     1    0.087 
                  14.0270   <br>
                       4      CCl4     1  TRS       C     2    0.055 
                  12.0110   <br>
                       5       CH2     1  TRS      C3     2    0.049 
                  14.0270   <br>
                       6        OA     1  TRS      O3     2   -0.205 
                  15.9994   <br>
                       7         H     1  TRS     H33     2    0.019  
                  1.0080   <br>
                       8        NL     1  TRS       N     2    0.206 
                  14.0067   <br>
                       9         H     1  TRS      H2     2    0.004  
                  1.0080   <br>
                      10         H     1  TRS      H3     2    0.004  
                  1.0080   <br>
                      11         H     1  TRS      H1     2    0.004  
                  1.0080   <br>
                      12       CH2     1  TRS      C2     2    0.050 
                  14.0270   <br>
                      13        OA     1  TRS      O2     2   -0.205 
                  15.9994   <br>
                      14         H     1  TRS     H23     2    0.019  
                  1.0080 <br>
                  ...<br>
                  <br>
                  <u><b>EDO.itp</b></u><br>
                  ...<br>
                  [ moleculetype ]<br>
                  ; Name nrexcl<br>
                  EDO      3<br>
                  <br>
                  [ atoms ]<br>
                  ;   nr      type  resnr resid  atom  cgnr   charge    
                  mass<br>
                       1        OA     1  EDO     OAB     1   -0.111 
                  15.9994   <br>
                       2         H     1  EDO     HAE     1    0.031  
                  1.0080   <br>
                       3       CH2     1  EDO     CAA     1    0.080 
                  14.0270   <br>
                       4       CH2     1  EDO     CAC     1    0.080 
                  14.0270   <br>
                       5        OA     1  EDO     OAD     1   -0.111 
                  15.9994   <br>
                       6         H     1  EDO     HAF     1    0.031  
                  1.0080 <br>
                  ...<br>
                  <u><b><br>
                      topol.top:</b></u><br>
                  ..<br>
                  ; Include water topology<br>
                  #include "gromos43a1.ff/spc.itp"<br>
                  #include "TRS.itp"<br>
                  #include "EDO.itp"<br>
                  ..<br>
                  [ molecules ]<br>
                  ; Compound        #mols<br>
                  Protein_chain_A     1<br>
                  Protein_chain_B     1<br>
                  SOL               185<br>
                  SOL               143<br>
                  TRS                1<br>
                  EDO                1<br>
                  SOL             44125<br>
                  <b><u><br>
                      Conf.gro:</u></b><br>
                  MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE<br>
                   5354<br>
                      2GLN      N    1   1.458  -1.158   0.739<br>
                      2GLN     H1    2   1.520  -1.083   0.763<br>
                  .......<br>
                    485HOH    HW1 5333   0.221  -3.864  -2.291<br>
                    485HOH    HW2 5334   0.303  -3.946  -2.407<br>
                      1TRS  O1       1  -3.812  -0.471  -2.002<br>
                      1TRS  H13      2  -3.865  -0.443  -1.922<br>
                      1TRS  C1       3  -3.672  -0.469  -1.971<br>
                      1TRS  C        4  -3.635  -0.571  -1.863<br>
                      1TRS  C3       5  -3.711  -0.547  -1.731<br>
                      1TRS  O3       6  -3.694  -0.414  -1.679<br>
                      1TRS  H33      7  -3.746  -0.404  -1.594<br>
                      1TRS  N        8  -3.673  -0.705  -1.911<br>
                      1TRS  H2       9  -3.625  -0.725  -1.996<br>
                      1TRS  H3      10  -3.771  -0.707  -1.927<br>
                      1TRS  H1      11  -3.649  -0.774  -1.842<br>
                      1TRS  C2      12  -3.483  -0.573  -1.840<br>
                      1TRS  O2      13  -3.428  -0.445  -1.806<br>
                      1TRS  H23     14  -3.470  -0.412  -1.722<br>
                      1EDO  OAB      1   0.307  -2.792   0.149<br>
                      1EDO  HAE      2   0.390  -2.826   0.104<br>
                      1EDO  CAA      3   0.239  -2.901   0.212<br>
                      1EDO  CAC      4   0.111  -2.851   0.281<br>
                      1EDO  OAD      5   0.144  -2.763   0.388<br>
                      1EDO  HAF      6   0.060  -2.731   0.432<br>
                     8.13100   7.04165  13.54850   0.00000   0.00000 
                  -4.06550   0.00000   0.00000   0.00000<br clear="all">
                  <br>
                  How can I fixed these notes(note 1 and note 2)?<br>
                  <br>
                  Thanks in advance<br>
                  -- <br>
                  Ahmet YILDIRIM<br>
                </blockquote>
                <br>
              </div>
            </div>
          </div>
          <br>
          --<br>
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        </blockquote>
      </div>
      <br>
      <br clear="all">
      <br>
      -- <br>
      Ahmet YILDIRIM<br>
    </blockquote>
    <br>
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