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On 4/19/2011 6:55 AM, Emine Deniz Tekin wrote:
<blockquote
cite="mid:BANLkTim24K+6SHpeFVs0T2x9Eph2crNiSA@mail.gmail.com"
type="cite">
<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.)</div>
</blockquote>
<br>
Looks about right.<br>
<br>
<blockquote
cite="mid:BANLkTim24K+6SHpeFVs0T2x9Eph2crNiSA@mail.gmail.com"
type="cite">
<div> 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>
</blockquote>
<br>
I don't know anything about those atom types or force field. Use
your own judgment.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTim24K+6SHpeFVs0T2x9Eph2crNiSA@mail.gmail.com"
type="cite">
<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=""> </span>[ atoms
]</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>CA<span
style=""> </span>LP2<span style=""> </span>0.00000<span
style=""> </span>0</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>CB<span
style=""> </span>LP2<span style=""> </span>0.00000<span
style=""> </span>1</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>CG<span
style=""> </span>LP2<span style=""> </span>0.00000<span
style=""> </span>2</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>CD<span
style=""> </span>LP2<span style=""> </span>0.00000<span
style=""> </span>3</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>CE<span
style=""> </span>LP3<span style=""> </span>0.00000<span
style=""> </span>4</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>C<span
style=""> </span>LC<span style=""> </span>0.450<span
style=""> </span>5</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>O<span
style=""> </span>LO<span style=""> </span>-0.450<span
style=""> </span>5</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>[ bonds
]</font></font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><font face="Calibri"><span style=""> </span>CA<span
style=""> </span>CB<span style=""> </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=""> </span>C<span
style=""> </span>CA<span style=""> </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=""> </span>CB<span
style=""> </span>CG<span style=""> </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=""> </span>CG<span
style=""> </span>CD<span style=""> </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=""> </span>CD<span
style=""> </span>CE<span style=""> </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=""> </span>C<span
style=""> </span>O<span style=""> </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=""> </span>C<span
style=""> </span>+N<span style=""> </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=""> </span>C<span style=""> </span><span
style=""> </span>CA<span style=""> </span>CB<span
style=""> </span>1 0.11100E+03 0.46020E+03</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>CA<span style=""> </span>CB<span
style=""> </span>CG<span style=""> </span>1
0.11100E+03 0.46020E+03</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>CB<span style=""> </span>CG<span
style=""> </span>CD<span style=""> </span>1
0.11100E+03 0.46020E+03</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>CG<span style=""> </span>CD<span
style=""> </span>CE<span style=""> </span>1
0.11100E+03 0.46020E+03</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>O<span style=""> </span>C<span
style=""> </span>CA<span style=""> </span>1
0.12100E+03 0.50210E+03</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>CA<span style=""> </span>C<span
style=""> </span>+N<span style=""> </span>ga_19</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>O<span style=""> </span>C<span
style=""> </span>+N<span style=""> </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=""> </span>C<span style=""> </span>CA<span
style=""> </span>CB<span style=""> </span>CG<span
style=""> </span>1<span style=""> </span>0.0<span
style=""> </span>5.86<span style=""> </span>3</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"> <font
size="3">CA<span style=""> </span>CB<span style="">
</span>CG<span style=""> </span>CD<span style="">
</span>3</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>CB<span style=""> </span>CG<span
style=""> </span>CD<span style=""> </span>CE<span
style=""> </span>3</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>[ impropers ]</font></p>
<p style="margin: 0cm 0cm 10pt;" class="MsoNormal"><font
size="3"><span style=""> </span>C<span style=""> </span>CA<span
style=""> </span>+N<span style=""> </span>O<span
style=""> </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 moz-do-not-send="true"
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: 1px solid rgb(204, 204, 204);
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 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;"><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;"><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;"><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 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
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote style="border-left: 1px solid rgb(204,
204, 204); 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: 1px solid rgb(204,
204, 204); 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>
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