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    On 1/07/2011 8:35 PM, Emine Deniz Tekin wrote:
    <blockquote
      cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
      type="cite">
      <p class="MsoNormal"><span style="font-size: 12pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">Hi Gromacs users,</span></p>
      <p class="MsoNormal"><span style="font-size: 12pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><br>
        </span></p>
      <p class="MsoNormal"><span style="font-size: 12pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">I created a lipopeptide
          (lauroic acid <span style=""> </span>connected to an
          8-residue peptide which starts
          with Valine).</span></p>
    </blockquote>
    <br>
    How is the link from acid to peptide created?<br>
    <br>
    <blockquote
      cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
      type="cite">
      <p class="MsoListParagraphCxSpFirst" style="text-indent: -18pt;"><span
          style="font-size: 12pt; line-height: 115%; font-family:
          Symbol;"><span style="">·<span style="font: 7pt &quot;Times
              New Roman&quot;;">        
            </span></span></span><span style="font-size: 12pt;
          line-height: 115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">If I try to use pdb2gmx with
          -ter
          flag<span style="">   </span>(Start terminus VAL-2: None, End
          terminus ASP-9: COO-), everything seems to work (topology is
          created.).</span></p>
    </blockquote>
    <br>
    Does that topology work for MD? Why does pdb2gmx think there's 9
    residues, and below there seem to be 63?<br>
    <br>
    <blockquote
      cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
      type="cite">
      <p class="MsoListParagraphCxSpMiddle" style="text-indent: -18pt;"><span
          style="font-size: 12pt; line-height: 115%; font-family:
          Symbol;"><span style="">·<span style="font: 7pt &quot;Times
              New Roman&quot;;">        
            </span></span></span><span style="font-size: 12pt;
          line-height: 115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">But, if I try to use pdb2gmx
          with -ter
          flag<span style="">  </span>for more than one lipopeptide at
          desired positions, it gives the following error. (again says
          Start terminus
          VAL-2: None, End terminus ASP-9: COO- )</span></p>
      <p class="MsoListParagraphCxSpLast"><span style="font-size: 12pt;
          line-height: 115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"> <b>Fatal error:  Atom N not
            found in residue <a moz-do-not-send="true"
              href="http://seq.nr">seq.nr</a>.
            1 while adding improper</b></span></p>
      <p class="MsoNormal"><span style="font-size: 12pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">While I was creating the
          lipopeptide, I introduced
          the lauroic acid as a pseudo amino acid (following Mark’s
          suggestion). So, I
          really do NOT have atom N in the first residue. I pasted a
          part of my gro file
          below.</span></p>
    </blockquote>
    <br>
    Some improper in your topology database entries wants a N atom that
    doesn't exist. Unfortunately, we don't have anywhere near enough
    information to guess why. pdb2gmx is trying to match your .rtp and
    specbond entries to your .gro file, but only seeing the latter can't
    help diagnose a mismatch. Some description of "desired positions" is
    also important.<br>
    <br>
    Also, giving full command lines are always preferred. You may not
    think anything significant is there, and you might be right, but if
    there *can* be something significant there, and we aren't given the
    chance to know whether it is present, we might just not bother to
    waste time guessing :)<br>
    <br>
    Mark<br>
    <br>
    <blockquote
      cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
      type="cite">
      <p class="MsoNormal"><br>
        <span style="font-size: 12pt; line-height: 115%; font-family:
          &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></p>
      <p class="MsoNormal">
      </p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">GROMACS molecule input test</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">574</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CA<span style="">   
          </span>1<span style="">  </span>11.027<span style="">   </span>5.295<span
            style="">  
          </span>3.153</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CB<span style="">   
          </span>2<span style="">  </span>10.894<span style="">   </span>5.299<span
            style="">  
          </span>3.078</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CG<span style="">   
          </span>3<span style="">  </span>10.777<span style="">   </span>5.234<span
            style="">  
          </span>3.153</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CD<span style="">   
          </span>4<span style="">  </span>10.645<span style="">   </span>5.254<span
            style="">  
          </span>3.078</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CE<span style="">   
          </span>5<span style="">  </span>10.521<span style="">   </span>5.203<span
            style="">  
          </span>3.153</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CZ<span style="">   
          </span>6<span style="">  </span>10.392<span style="">   </span>5.251<span
            style="">  
          </span>3.086</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CM<span style="">   
          </span>7<span style="">  </span>10.266<span style="">   </span>5.207<span
            style="">  
          </span>3.161</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CN<span style="">   
          </span>8<span style="">  </span>10.140<span style="">   </span>5.272<span
            style="">  
          </span>3.103</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CO<span style="">   
          </span>9<span style="">  </span>10.014<span style="">   </span>5.221<span
            style="">  
          </span>3.172</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CP<span style="">  
          </span>10<span style="">   </span>9.885<span style="">   </span>5.279<span
            style="">  
          </span>3.112</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">     </span>CQ<span style="">  
          </span>11<span style="">   </span>9.761<span style="">   </span>5.203<span
            style="">  
          </span>3.160</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style=""> </span><span
            style="">   </span>1DPP<span style="">     
          </span>C<span style="">   </span>12<span style="">  </span>11.101<span
            style="">  
          </span>5.430<span style="">   </span>3.147</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>1DPP<span
            style="">      </span>O<span style="">  
          </span>13<span style="">  </span>11.032<span style="">   </span>5.531<span
            style="">  
          </span>3.136</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">      </span>N<span style="">  
          </span>14<span style="">  </span>11.235<span style="">   </span>5.450<span
            style="">  
          </span>3.160</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">      </span>H<span style="">  
          </span>15<span style="">  </span>11.249<span style="">   </span>5.550<span
            style="">  
          </span>3.159</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">     </span>CA<span style="">  
          </span>16<span style="">  </span>11.368<span style="">   </span>5.385<span
            style="">  
          </span>3.181</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">     </span>CB<span style="">  
          </span>17<span style="">  </span>11.390<span style="">   </span>5.233<span
            style="">  
          </span>3.181</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">    </span>CG1<span style="">  
          </span>18<span style="">  </span>11.332<span style="">   </span>5.172<span
            style="">  
          </span>3.308</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">    </span>CG2<span style="">  
          </span>19<span style="">  </span>11.338<span style="">   </span>5.161<span
            style="">  
          </span>3.056</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">      </span>C<span style="">  
          </span>20<span style="">  </span>11.486<span style="">   </span>5.449<span
            style="">  
          </span>3.103</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>2VAL<span
            style="">      </span>O<span style="">  
          </span>21<span style="">  </span>11.498<span style="">   </span>5.436<span
            style="">  
          </span>2.982</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">    </span>…………..</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">   </span>63ASP<span
            style="">    </span>OD1<span style=""> 
          </span>570<span style="">  </span>-0.306<span style="">  </span>14.874<span
            style="">  
          </span>3.343</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">   </span>63ASP<span
            style="">    </span>OD2<span style=""> 
          </span>571<span style="">  </span>-0.451<span style="">  </span>15.030<span
            style="">  
          </span>3.289</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">   </span>63ASP<span
            style="">      </span>C<span style=""> 
          </span>572<span style="">  </span>-0.057<span style="">  </span>15.023<span
            style="">  
          </span>3.106</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">   </span>63ASP<span
            style="">     </span>O1<span style=""> 
          </span>573<span style="">   </span>0.014<span style="">  </span>15.003<span
            style="">  
          </span>3.207</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style="">   </span>63ASP<span
            style="">     </span>O2<span style=""> 
          </span>574<span style="">  </span>-0.029<span style="">  </span>15.104<span
            style="">  
          </span>3.017</span></p>
      <p class="MsoNormal"><span style="font-size: 9pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;"><span style=""> 
          </span>16.23937<span style="">   </span>16.23937<span
            style="">   </span>16.23937</span></p>
      <p class="MsoNormal"><br>
        <span style="font-size: 9pt; line-height: 115%; font-family:
          &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></p>
      <p class="MsoNormal">
      </p>
      <p class="MsoNormal"><span style="font-size: 12pt; line-height:
          115%; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">I am using Gromacs 53a6 force
          field and gromacs
          4.5.3 version.</span></p>
      <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
        normal;"><span style="font-size: 12pt; font-family: &quot;Times
          New Roman&quot;,&quot;serif&quot;;">Any help will be
          appreciated.</span></p>
      <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
        normal;"><span style="font-size: 12pt; font-family: &quot;Times
          New Roman&quot;,&quot;serif&quot;;"> </span><span
          style="font-size: 12pt; font-family: &quot;Times New
          Roman&quot;,&quot;serif&quot;;">Thanks in advance</span>
      </p>
      <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
        normal;"><span style="font-size: 12pt; font-family: &quot;Times
          New Roman&quot;,&quot;serif&quot;;"> </span></p>
      <p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height:
        normal;"><span style="font-size: 12pt; font-family: &quot;Times
          New Roman&quot;,&quot;serif&quot;;">Deniz</span></p>
    </blockquote>
    <br>
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