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On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
<blockquote
cite="mid:BANLkTikUoJsmXb+qqnkr3PnhHPDyR02H3w@mail.gmail.com"
type="cite"><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 "Times New Roman";">
</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>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:BANLkTikUoJsmXb+qqnkr3PnhHPDyR02H3w@mail.gmail.com"
type="cite">
<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 "Times New Roman";">
</span></span></span><span style="" lang="EN-US">I
added the lauroic acid as a "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 "Times New Roman";"> </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:
"Arial","sans-serif"; 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 </span></p>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:BANLkTikUoJsmXb+qqnkr3PnhHPDyR02H3w@mail.gmail.com"
type="cite">
<p class="MsoListParagraph" style="margin-left: 54pt; text-indent:
-18pt;"><span style="" 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 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: "Calibri","sans-serif";"
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>
</blockquote>
<br>
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>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikUoJsmXb+qqnkr3PnhHPDyR02H3w@mail.gmail.com"
type="cite">
<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"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></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 "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">
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</font></blockquote>
</div>
<br>
</blockquote>
<br>
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