<p class="MsoNormal"><font size="4"><span style="line-height: 115%; font-family: "Times New Roman","serif";">Hi Mark,</span></font></p><font size="4">
</font><p class="MsoNormal"><font size="4"><span style="line-height: 115%; font-family: "Times New Roman","serif";">Thank you for your reply.</span></font></p><font size="4">
</font><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><font size="4"><span style="font-family: "Times New Roman","serif";">Let me
explain the problem a little more and answer your questions. I would be happy
if you could expound upon your reply.</span></font></p><pre><span style="font-size:12.0pt;font-family:"Times New Roman","serif""><span style="color:black;mso-themecolor:text1"></span></span> <font size="2">Hi Gromacs users,</font></pre>
<font size="2"><span style="line-height: 115%; font-family: "Times New Roman","serif";"></span></font><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im"><blockquote type="cite"><font size="2"><span style="line-height: 115%; font-family: "Times New Roman","serif";">I created a lipopeptide
(lauroic acid <span> </span>connected to an
8-residue peptide which starts
with Valine).</span>
</font></blockquote><font size="2">
<span style="color: rgb(255, 0, 0);">How is the link from acid to peptide created?</span></font></div><div class="im"><br>
<font size="4"><span style="font-family: "Times New Roman","serif"; color: black;">The link between acid and peptide is a “peptide bond”. </span></font><pre><font size="4"><span style="font-family: "Times New Roman","serif"; color: black;">(<span>I prepared the *rtp *entry for the lauroic acid make a peptide bond as if lauroic acid was an amino acid (following your suggestion)).</span></span></font></pre>
<br>
<span style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol;mso-fareast-language:TR"><span style="mso-list:
Ignore"><span style="font:7.0pt "Times New Roman""> </span></span></span><font size="4"><span style="font-family: "Times New Roman","serif";">If I try to
use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is</span>
</font>
<p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><font size="4"><span style="font-family: "Times New Roman","serif";"><span> </span>pdb2gmx –f one_lipopeptide.pdb
-ter </span></font></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman";mso-fareast-language:TR"></span><font size="4">It seems to work. That is,
topol.top is created. (And also this <span style="color: rgb(51, 51, 51);">topology works <span> </span>for MD.</span>)</font></p><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman";mso-fareast-language:TR"><span style="color:red"></span></span><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal">
</p><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman";mso-fareast-language:TR"> </span></p>
</div>
<font size="2"><span style="color: rgb(255, 0, 0);">Does that topology work for MD? Why does pdb2gmx think there's 9
residues, and below there seem to be 63?</span></font></div></blockquote><div>
<p class="MsoListParagraphCxSpFirst" style="margin-bottom:0cm;margin-bottom:.0001pt;
mso-add-space:auto;text-indent:-18.0pt;line-height:normal;mso-list:l0 level1 lfo1"><span style="font-size:12.0pt;font-family:Symbol;mso-fareast-font-family:Symbol;
mso-bidi-font-family:Symbol;mso-fareast-language:TR"><span style="mso-list:
Ignore">·<span style="font:7.0pt "Times New Roman""> </span></span></span><font size="4"><span style="font-family: "Times New Roman","serif";">But, if I
try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at desired positions (63 residues),
that is</span></font></p><font size="4">
</font><p class="MsoNormal" style="margin-bottom: 0.0001pt; line-height: normal;"><font size="4"><span style="font-family: "Times New Roman","serif";"><span> </span>pdb2gmx –f seven_lipopeptide.pdb
-ter </span></font></p><font size="4">
</font>
<span style="font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman";mso-ansi-language:TR;mso-fareast-language:
TR;mso-bidi-language:AR-SA"><span style="mso-spacerun:yes"> </span><font size="4">It gives the fatal error: <span style="color: black;">“<span>Atom N not found in residue </span></span></font></span><font size="4"><span style="line-height: 115%; font-family: "Calibri","sans-serif";"><a href="http://seq.nr/" target="_blank"><span style="line-height: 115%; font-family: "Times New Roman","serif"; color: black;">seq.nr</span></a></span><span style="line-height: 115%; font-family: "Times New Roman","serif"; color: black;">. 1 while adding improper”</span></font>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div text="#000000" bgcolor="#ffffff"><div class="im"><blockquote type="cite"><p class="MsoNormal">
<span style="font-size:12pt;line-height:115%;font-family:Symbol"><span><span style="font:7pt "Times New Roman""></span></span></span><font size="2"><span style="line-height: 115%; font-family: "Times New Roman","serif";">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></font></p>
</blockquote>
</div><font size="2">
</font><font size="1"><font style="color: rgb(255, 0, 0);" size="2">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.</font><br></font></div></blockquote><div><br>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";
mso-fareast-font-family:"Times New Roman";color:black;mso-themecolor:text1;
mso-fareast-language:TR;mso-bidi-font-weight:bold"> <font size="4">I wrote <span> </span>a code to put 7 identical lipopeptides at
desired positions. That is, 7 lipopeptides are placed on a plane with 15 degree
angle between the adjacent lipopeptides.</font></span><span style="font-size:12.0pt;
font-family:"Times New Roman","serif";mso-fareast-font-family:"Times New Roman";
color:black;mso-themecolor:text1;mso-fareast-language:TR"></span></p>
<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 text="#000000" bgcolor="#ffffff"><font size="1"></font>
<br>
<span style="color: rgb(255, 0, 0);">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 :)</span><br style="color: rgb(255, 0, 0);"></div></blockquote><div><br><font size="4">I used gromos53a6 force field (extended to </font><font size="4"><font face="Arial">include</font> lauroic acid parameters) & spc type water <br>
<br></font></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div text="#000000" bgcolor="#ffffff"><font color="#888888"><font size="4">
</font><br>
</font></div></blockquote><div>
<font size="4"><span style="font-family: "Times New Roman","serif"; color: rgb(0, 0, 0);">And also, I have a question: The first residue in my pdb file is lauroic acid that is DPP, second residue is Valine and so on.. But when I used the
pdb2gmx with –ter it says: Start terminus VAL-2: None, End terminus ASP-9:
COO-) Would not DPP residue be the start terminus?<br><br></span></font><font size="4">Best regards,</font></div><div><font color="#888888"><br>Mark</font> <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 text="#000000" bgcolor="#ffffff"><div><div class="h5">
Deniz<br>
<blockquote type="cite">
<p class="MsoNormal"><br>
<span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif""></span></p>
<p class="MsoNormal">
</p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif"">GROMACS molecule input test</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif"">574</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CA<span>
</span>1<span> </span>11.027<span> </span>5.295<span>
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CB<span>
</span>2<span> </span>10.894<span> </span>5.299<span>
</span>3.078</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CG<span>
</span>3<span> </span>10.777<span> </span>5.234<span>
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CD<span>
</span>4<span> </span>10.645<span> </span>5.254<span>
</span>3.078</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CE<span>
</span>5<span> </span>10.521<span> </span>5.203<span>
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CZ<span>
</span>6<span> </span>10.392<span> </span>5.251<span>
</span>3.086</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CM<span>
</span>7<span> </span>10.266<span> </span>5.207<span>
</span>3.161</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CN<span>
</span>8<span> </span>10.140<span> </span>5.272<span>
</span>3.103</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CO<span>
</span>9<span> </span>10.014<span> </span>5.221<span>
</span>3.172</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CP<span>
</span>10<span> </span>9.885<span> </span>5.279<span>
</span>3.112</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>CQ<span>
</span>11<span> </span>9.761<span> </span>5.203<span>
</span>3.160</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span><span> </span>1DPP<span>
</span>C<span> </span>12<span> </span>11.101<span>
</span>5.430<span> </span>3.147</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>1DPP<span> </span>O<span>
</span>13<span> </span>11.032<span> </span>5.531<span>
</span>3.136</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>N<span>
</span>14<span> </span>11.235<span> </span>5.450<span>
</span>3.160</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>H<span>
</span>15<span> </span>11.249<span> </span>5.550<span>
</span>3.159</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>CA<span>
</span>16<span> </span>11.368<span> </span>5.385<span>
</span>3.181</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>CB<span>
</span>17<span> </span>11.390<span> </span>5.233<span>
</span>3.181</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>CG1<span>
</span>18<span> </span>11.332<span> </span>5.172<span>
</span>3.308</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>CG2<span>
</span>19<span> </span>11.338<span> </span>5.161<span>
</span>3.056</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>C<span>
</span>20<span> </span>11.486<span> </span>5.449<span>
</span>3.103</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>2VAL<span> </span>O<span>
</span>21<span> </span>11.498<span> </span>5.436<span>
</span>2.982</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>…………..</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>63ASP<span> </span>OD1<span>
</span>570<span> </span>-0.306<span> </span>14.874<span>
</span>3.343</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>63ASP<span> </span>OD2<span>
</span>571<span> </span>-0.451<span> </span>15.030<span>
</span>3.289</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>63ASP<span> </span>C<span>
</span>572<span> </span>-0.057<span> </span>15.023<span>
</span>3.106</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>63ASP<span> </span>O1<span>
</span>573<span> </span>0.014<span> </span>15.003<span>
</span>3.207</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span> </span>63ASP<span> </span>O2<span>
</span>574<span> </span>-0.029<span> </span>15.104<span>
</span>3.017</span></p>
<p class="MsoNormal"><span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""><span>
</span>16.23937<span> </span>16.23937<span> </span>16.23937</span></p>
<p class="MsoNormal"><br>
<span style="font-size:9pt;line-height:115%;font-family:"Times New Roman","serif""></span></p>
<p class="MsoNormal">
</p>
<p class="MsoNormal"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman","serif"">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:"Times New Roman","serif"">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:"Times New Roman","serif""> </span><span style="font-size:12pt;font-family:"Times New Roman","serif"">Thanks in advance</span>
</p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif""> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:12pt;font-family:"Times New Roman","serif"">Deniz</span></p>
</blockquote>
<br>
</div></div></div>
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