<br>

<p class="MsoNormal"><span style="" lang="EN-US">Hi Mark,</span></p>

<p class="MsoNormal"><span style="" lang="EN-US"><br></span></p><p class="MsoNormal"><span style="" lang="EN-US">Thank you
for your reply. But, I couldn’t understand very well what you meant <span style="color: red;">“</span></span><span style="color: red;">you can make one that
uses backbone-style linking. Most of the forcefields will have examples of
non-amino-acid terminating residues - these make a single peptide bond just
like yours does.</span><span style="color: red;" lang="EN-US">”.</span><span style="" lang="EN-US"> So, let me
explain the problem a little more.<span style="">  </span>I
would be happy if you could expound upon your reply. <br></span></p><p class="MsoNormal"><br><span style="" lang="EN-US"></span></p><p class="MsoNormal">

</p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;"><span style="" lang="EN-US"><span style=""><b>1)</b><span style="font: 7pt &quot;Times New Roman&quot;;">     
</span></span></span><span style="" lang="EN-US">I
prepared the <b>rtp </b>entry for the lauroic acid (see below) and add the lipid
parameters to the relevant sections of the <b style="">ffnonbonded.itp</b>
and <b style="">ffbonded.itp</b> files.</span></p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;">

</p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;"><span style="" lang="EN-US"><span style=""><b>2)</b><span style="font: 7pt &quot;Times New Roman&quot;;">     
</span></span></span><span style="" lang="EN-US">I
added the lauroic acid as a &quot;Non-Protein” in the <b style="">residuetypes.dat<span style=""> </span></b>file and also
I introduced the atom types (LO<span style="">: </span>15.9994,
LC:<span style=""> </span>12.0110, LP2<span style="">: </span>14.0270, LP3<span style="">: </span>15.0350) in the <span style=""></span><b style="">atomtypes.atp.</b></span></p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;">


</p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;"><b style=""><span style="" lang="EN-US"><span style="">3)<span style="font: 7pt &quot;Times New Roman&quot;;">      </span></span></span></b><span style="" lang="EN-US">I concatenated<span style=""> </span>the structure files of a 8-residue-peptide<b style=""> </b>and lauroic acid as <b style="">system.gro. </b></span><span style="font-size: 10pt; line-height: 115%; font-family: &quot;Arial&quot;,&quot;sans-serif&quot;; color: black;">Then, using “pdb2gmx -ter”, I obtained the <b>topol.top, conf.gro</b> and
<b>posre.itp</b> for <b style="">the whole system.</b> </span><span style="" lang="EN-US">(I chose : start terminus VAL-2: NH2 and end terminus ASP-9: COO-) </span>

</p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;"><span style="" lang="EN-US"></span><span style="" lang="EN-US"> <b>4)</b>   But
when I looked into <b>conf.gro</b> with the VMD, I see that the peptide bond is formed
between the lauroic acid (C34) and the N terminal of the Valine. However,
second H of the N is still there and it is making another bond with C34 of
lauroic acid. <span style=""></span>The strange thing is: C34
is double bonded to O35,</span><span lang="EN-US"> </span><span style="" lang="EN-US">Carbon makes four bonds. <br></span></p><p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;"><span style="font-size: 11pt; line-height: 115%; font-family: &quot;Calibri&quot;,&quot;sans-serif&quot;;" lang="EN-US">How can I get rid of that H?</span></p>
<p class="MsoListParagraph" style="margin-left: 54pt; text-indent: -18pt;">

</p><p class="MsoListParagraphCxSpFirst" style="margin-left: 54pt;"><span style="" lang="EN-US">[ DPP ]</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style=""> </span>[ atoms ]</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C34<span style="">      
</span>LC<span style="">     </span>0.800<span style="">    </span>18</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>O35<span style="">      
</span>LO<span style="">    </span>-0.60<span style="">     </span>18</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C36<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>19</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C37<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>20</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C38<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>21</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C39<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>22</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C40<span style="">     
</span>LP2<span style="">      </span>0 <span style="">      </span>23</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C41<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>24</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C42<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>25</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C43<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>26</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C44<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>27</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>C45<span style="">     
</span>LP2<span style="">      </span>0<span style="">       </span>28</span></p>

<p class="MsoListParagraphCxSpLast" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">  
</span>C46<span style="">      </span>LP3<span style="">      </span>0<span style="">      
</span>29</span> 



</p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US">[ bonds ]</span></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US">;<span style="">  </span>ai<span style="">   
</span>aj funct</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>34<span style="">     
</span>35<span style="">       </span>1 0.12300E+00 0.50210E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>34<span style="">     
</span>36<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>36<span style="">     
</span>37<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>37<span style="">     
</span>38<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>38<span style="">     
</span>39<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>39<span style="">     
</span>40<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>40<span style="">     
</span>41<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>41<span style="">     
</span>42<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>42<span style="">     
</span>43<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>43<span style="">     
</span>44<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>44<span style="">     
</span>45<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>45<span style="">     
</span>46<span style="">       </span>1 0.15300E+00 0.33470E+06</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US">[ angles ]</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US">;<span style="">  </span>ai<span style="">   
</span>aj<span style="">    </span>ak funct</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>34<span style="">     
</span>36<span style="">      </span>37<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>35<span style="">     
</span>34<span style="">      </span>36<span style="">       </span>1 0.12100E+03 0.50210E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>36<span style="">     
</span>37<span style="">      </span>38<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>37<span style="">     
</span>38<span style="">      </span>39<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>38<span style="">     
</span>39<span style="">      </span>40<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>39<span style="">     
</span>40<span style="">      </span>41<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>40<span style="">     
</span>41<span style="">      </span>42<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>41<span style="">     
</span>42<span style="">      </span>43<span style="">    </span><span style="">   </span>1
0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>42<span style="">     
</span>43<span style="">      </span>44<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>43<span style="">     
</span>44<span style="">      </span>45<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p>





<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">      </span>44<span style="">     
</span>45<span style="">      </span>46<span style="">       </span>1 0.11100E+03 0.46020E+03</span></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US">[ dihedrals ]</span></p>


<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US">;<span style="">  </span>ai<span style="">   
</span>aj<span style="">    </span>ak<span style="">    </span>al funct<span style="">  
</span>phi0<span style="">     </span>cp<span style="">     </span>mult</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>34<span style="">   
</span>36<span style="">    </span>37<span style="">    </span>38<span style="">    
</span>1<span style="">    </span>0.0<span style="">     </span>5.86<span style="">   
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>36<span style="">   
</span>37<span style="">    </span>38<span style="">    </span>39<span style="">    
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>37<span style="">   
</span>38<span style="">    </span>39<span style="">    </span>40<span style="">    
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>38<span style="">   
</span>39<span style="">    </span>40<span style="">    </span>41<span style="">    
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>39<span style="">   
</span>40<span style="">    </span>41<span style="">    </span>42<span style="">    
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>40<span style="">   
</span>41<span style="">    </span>42<span style="">    </span>43<span style="">    
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>41<span style="">   
</span>42<span style="">    </span>43<span style="">    </span>44<span style="">    
</span>3</span></p>

<p class="MsoListParagraphCxSpMiddle" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">   </span>42<span style="">   
</span>43<span style="">  </span><span style="">  </span>44<span style="">   
</span>45<span style="">     </span>3</span></p>

<p class="MsoListParagraphCxSpLast" style="margin-left: 54pt;"><span style="" lang="EN-US"><span style="">  
</span>43<span style="">    </span>44<span style="">    </span>45<span style="">   
</span>46<span style="">     </span>3</span></p><p class="MsoListParagraphCxSpLast" style="margin-left: 54pt;"><br><span style="" lang="EN-US"></span></p><p class="MsoListParagraphCxSpLast" style="margin-left: 54pt;"><span style="" lang="EN-US">Best regards,</span></p>
<p class="MsoListParagraphCxSpLast" style="margin-left: 54pt;"><span style="" lang="EN-US">Deniz<br></span></p>

   











<br><br><br><br><div class="gmail_quote">On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham <span dir="ltr">&lt;<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
Hi Gromacs users,<br>
<br>
I want to covalently link the lauroic acid to the Valine residue (it is a peptide (amide) bond), I know that I should update the specbond.dat.But before updating this file, I need the NH as an N terminal of the first residue (Valine).When I used pdb2gmx with the –ter flag, I got either NH3, NH2 or None instead of NH.So, I add the [NH] directive in the aminoacids.n.rtp file, as follows;<br>

<br>
<br>
[ NH ]<br>
<br>
[ replace ]<br>
<br>
; old-namenew-typenew-massnew-charge<br>
<br>
NLN14.0067-0.31<br>
<br>
CACH113.0190.127<br>
<br>
[ add ]<br>
<br>
12HNCAC<br>
<br>
;atom_typemasscharge<br>
<br>
H1.0080.31<br>
<br>
[ delete ]<br>
<br>
H<br>
<br>
[ bonds ]<br>
<br>
NHgb_2<br>
<br>
[ angles ]<br>
<br>
CANHga_11<br>
<br>
[ dihedrals ]<br>
<br></div>
HNCACgd_29<div class="im"><br>
<br>
<br>
(ps. I wrote the charges of N, CA and H according to values defined in topol.top and also I used the Gromos96 53a6 force field)<br>
<br>
<br>
Then, I used the pdb2gmx with –ter, I could see:<br>
<br>
Select start terminus type for VAL<br>
<br>
0: NH<br>
<br>
1: NH3+<br>
<br>
2: NH2<br>
<br>
3: None<br>
<br>
<br></div>
Finally, I got thetopol.top, posre itp and conf.gro files. But when I looked into conf.gro, I see that I am getting “None”. How can I get the NH ?<br>
<br>
</blockquote>
<br>
Coordinating multiple &quot;moving parts&quot; like the specbond and terminus-fixing is probably a recipe for trouble.<br>
<br>
Since you have to make an .rtp entry for lauroic acid anyway, you can make one that uses backbone-style linking. Most of the forcefields will have examples of non-amino-acid terminating residues - these make a single peptide bond just like yours does. Now you can ignore the specbond and terminus-fixing mechanisms entirely.<br>

<br>
Mark<br><font color="#888888">
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