<div>Hi Mark,</div>
<div> </div>
<div>Thanks again. Your suggestion of introducing the lauroic acid as a pseudo-amino acid seems to solve my problem. Below is my corrected "aminoacids.rtp" file for the 6-Carbon case as a test. (I used the Berger lipid parameters.) Just to be sure, could you have a look at the file (I used gb_10 between C and +N instead of gb_19). </div>
<div> </div>
<div>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri">[ DPP ]</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>[ atoms ]</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>LP2<span style="mso-spacerun: yes"> </span>0.00000<span style="mso-spacerun: yes"> </span>0</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>LP2<span style="mso-spacerun: yes"> </span>0.00000<span style="mso-spacerun: yes"> </span>1</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>LP2<span style="mso-spacerun: yes"> </span>0.00000<span style="mso-spacerun: yes"> </span>2</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>LP2<span style="mso-spacerun: yes"> </span>0.00000<span style="mso-spacerun: yes"> </span>3</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CE<span style="mso-spacerun: yes"> </span>LP3<span style="mso-spacerun: yes"> </span>0.00000<span style="mso-spacerun: yes"> </span>4</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>LC<span style="mso-spacerun: yes"> </span>0.450<span style="mso-spacerun: yes"> </span>5</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>O<span style="mso-spacerun: yes"> </span>LO<span style="mso-spacerun: yes"> </span>-0.450<span style="mso-spacerun: yes"> </span>5</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>[ bonds ]</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>1 0.15300E+00 0.33470E+06</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>1 0.15300E+00 0.33470E+06</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>1 0.15300E+00 0.33470E+06</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>1 0.15300E+00 0.33470E+06</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>CE<span style="mso-spacerun: yes"> </span>1 0.15300E+00 0.33470E+06</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>O<span style="mso-spacerun: yes"> </span>1 0.12300E+00 0.50210E+06</font></font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><font face="Calibri"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>+N<span style="mso-spacerun: yes"> </span>gb_10</font></font></p>
<font face="Calibri">
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">[ angles ]</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span><span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>1 0.11100E+03 0.46020E+03</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>1 0.11100E+03 0.46020E+03</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>1 0.11100E+03 0.46020E+03</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>CE<span style="mso-spacerun: yes"> </span>1 0.11100E+03 0.46020E+03</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>O<span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>1 0.12100E+03 0.50210E+03</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>+N<span style="mso-spacerun: yes"> </span>ga_19</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>O<span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>+N<span style="mso-spacerun: yes"> </span>ga_33</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3">[ dihedrals ]</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>1<span style="mso-spacerun: yes"> </span>0.0<span style="mso-spacerun: yes"> </span>5.86<span style="mso-spacerun: yes"> </span>3</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"> <font size="3">CA<span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>3</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>CB<span style="mso-spacerun: yes"> </span>CG<span style="mso-spacerun: yes"> </span>CD<span style="mso-spacerun: yes"> </span>CE<span style="mso-spacerun: yes"> </span>3</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>[ impropers ]</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="3"><span style="mso-spacerun: yes"> </span>C<span style="mso-spacerun: yes"> </span>CA<span style="mso-spacerun: yes"> </span>+N<span style="mso-spacerun: yes"> </span>O<span style="mso-spacerun: yes"> </span>gi_1</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="4">Best regards,</font></p>
<p style="MARGIN: 0cm 0cm 10pt" class="MsoNormal"><font size="4">Deniz</font></p></font></div>
<div> </div>
<div>On Tue, Apr 12, 2011 at 4:26 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br></div>
<div class="gmail_quote">
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div bgcolor="#ffffff" text="#000000">
<div class="im">On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
<blockquote type="cite"><br>
<p class="MsoNormal"><span lang="EN-US">Hi Mark,</span></p>
<p class="MsoNormal"><span lang="EN-US"><br></span></p>
<p class="MsoNormal"><span 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 lang="EN-US"> So, let me explain the problem a little more.<span> </span>I would be happy if you could expound upon your reply. <br>
</span></p>
<p class="MsoNormal"><br><span lang="EN-US"></span></p>
<p class="MsoNormal"></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span><b>1)</b><span style="FONT: 7pt 'Times New Roman'"> </span></span></span><span 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>ffnonbonded.itp</b> and <b>ffbonded.itp</b> files.</span></p>
</blockquote><br></div>That is not an .rtp entry, see below. Look at some .rtp entries and see how they make backbone bonds. That is what I understand you want to do - make a peptide bond as if lauroic acid was an amino acid.
<div class="im"><br><br>
<blockquote type="cite">
<p style="MARGIN-LEFT: 54pt"></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span><b>2)</b><span style="FONT: 7pt 'Times New Roman'"> </span></span></span><span lang="EN-US">I added the lauroic acid as a "Non-Protein” in the <b>residuetypes.dat<span> </span></b>file and also I introduced the atom types (LO<span>: </span>15.9994, LC:<span> </span>12.0110, LP2<span>: </span>14.0270, LP3<span>: </span>15.0350) in the <span></span><b>atomtypes.atp.</b></span></p>
<p style="MARGIN-LEFT: 54pt"></p>
<p style="MARGIN-LEFT: 54pt"><b><span lang="EN-US"><span>3)<span style="FONT: 7pt 'Times New Roman'"> </span></span></span></b><span lang="EN-US">I concatenated<span> </span>the structure files of a 8-residue-peptide<b> </b>and lauroic acid as <b>system.gro. </b></span><span style="LINE-HEIGHT: 115%; COLOR: black; FONT-SIZE: 10pt">Then, using “pdb2gmx -ter”, I obtained the <b>topol.top, conf.gro</b> and <b>posre.itp</b> for <b>the whole system.</b> </span><span lang="EN-US">(I chose : start terminus VAL-2: NH2 and end terminus ASP-9: COO-) </span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"></span><span 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 </span></p></blockquote><br></div>
No bond shown by VMD is relevant. It's guessing based on the coordinates in your .gro file. Your bonded atoms are in your .top file. VMD knows nothing about your .top file.
<div class="im"><br><br>
<blockquote type="cite">
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">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></span>The strange thing is: C34 is double bonded to O35,</span><span lang="EN-US"> </span><span lang="EN-US">Carbon makes four bonds. <br>
</span></p>
<p style="MARGIN-LEFT: 54pt"><span style="LINE-HEIGHT: 115%; FONT-SIZE: 11pt" lang="EN-US">How can I get rid of that H?</span></p>
<p style="MARGIN-LEFT: 54pt"></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">[ DPP ]</span></p></blockquote><br></div>This is not an .rtp entry. The [bonds] section must refer to atom names. I can only suppose pdb2gmx is warning about or ignoring everything after your [atoms] section.<br>
<br>Look in the .rtp and chapter 5 of the manual how terminating pseudo-residues like ACE work. Do something analogous for lauroic acid.<br><font color="#888888"><br>Mark</font>
<div>
<div></div>
<div class="h5"><br><br>
<blockquote type="cite">
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>[ atoms ]</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C34<span> </span>LC<span> </span>0.800<span> </span>18</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>O35<span> </span>LO<span> </span>-0.60<span> </span>18</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C36<span> </span>LP2<span> </span>0<span> </span>19</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C37<span> </span>LP2<span> </span>0<span> </span>20</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C38<span> </span>LP2<span> </span>0<span> </span>21</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C39<span> </span>LP2<span> </span>0<span> </span>22</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C40<span> </span>LP2<span> </span>0 <span> </span>23</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C41<span> </span>LP2<span> </span>0<span> </span>24</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C42<span> </span>LP2<span> </span>0<span> </span>25</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C43<span> </span>LP2<span> </span>0<span> </span>26</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C44<span> </span>LP2<span> </span>0<span> </span>27</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C45<span> </span>LP2<span> </span>0<span> </span>28</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>C46<span> </span>LP3<span> </span>0<span> </span>29</span> </p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">[ bonds ]</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">;<span> </span>ai<span> </span>aj funct</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>34<span> </span>35<span> </span>1 0.12300E+00 0.50210E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>34<span> </span>36<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>36<span> </span>37<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>37<span> </span>38<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>38<span> </span>39<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>39<span> </span>40<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>40<span> </span>41<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>41<span> </span>42<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>42<span> </span>43<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>43<span> </span>44<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>44<span> </span>45<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>45<span> </span>46<span> </span>1 0.15300E+00 0.33470E+06</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">[ angles ]</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">;<span> </span>ai<span> </span>aj<span> </span>ak funct</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>34<span> </span>36<span> </span>37<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>35<span> </span>34<span> </span>36<span> </span>1 0.12100E+03 0.50210E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>36<span> </span>37<span> </span>38<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>37<span> </span>38<span> </span>39<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>38<span> </span>39<span> </span>40<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>39<span> </span>40<span> </span>41<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>40<span> </span>41<span> </span>42<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>41<span> </span>42<span> </span>43<span> </span><span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>42<span> </span>43<span> </span>44<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>43<span> </span>44<span> </span>45<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>44<span> </span>45<span> </span>46<span> </span>1 0.11100E+03 0.46020E+03</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">[ dihedrals ]</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">;<span> </span>ai<span> </span>aj<span> </span>ak<span> </span>al funct<span> </span>phi0<span> </span>cp<span> </span>mult</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>34<span> </span>36<span> </span>37<span> </span>38<span> </span>1<span> </span>0.0<span> </span>5.86<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>36<span> </span>37<span> </span>38<span> </span>39<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>37<span> </span>38<span> </span>39<span> </span>40<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>38<span> </span>39<span> </span>40<span> </span>41<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>39<span> </span>40<span> </span>41<span> </span>42<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>40<span> </span>41<span> </span>42<span> </span>43<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>41<span> </span>42<span> </span>43<span> </span>44<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>42<span> </span>43<span> </span><span> </span>44<span> </span>45<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US"><span> </span>43<span> </span>44<span> </span>45<span> </span>46<span> </span>3</span></p>
<p style="MARGIN-LEFT: 54pt"><br><span lang="EN-US"></span></p>
<p style="MARGIN-LEFT: 54pt"><span lang="EN-US">Best regards,</span></p>
<p style="MARGIN-LEFT: 54pt"><span 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"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div>On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:<br></div>
<blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div><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><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 "moving parts" 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">-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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