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On 4/07/2011 11:49 PM, Emine Deniz Tekin wrote:
<blockquote
cite="mid:CAG7W+One1ppCdt0QKFiAfb4Cd_cEmT+ARFD00Tg0SLVC1Gef-A@mail.gmail.com"
type="cite">
<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>
</blockquote>
<br>
Sorry, I can't.<br>
<br>
* I won't try to make sense of five different font styles and a
forest of differential indentation.<br>
* You didn't say whether you tested the single lipopeptide topology
like I suggested. Solve simple problems completely before tackling
complex problems.<br>
* I pointed out that showing us only the coordinate file was not an
effective way of diagnosing a mismatch of topology database and
coordinate file naming, and you still haven't supplied any topology
information.<br>
* The *geometry* of the lipopetides is often irrelevant for trying
to get pdb2gmx to construct a *topology*<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAG7W+One1ppCdt0QKFiAfb4Cd_cEmT+ARFD00Tg0SLVC1Gef-A@mail.gmail.com"
type="cite">
<pre><span style="font-size: 12pt; font-family: "Times New Roman","serif";"><span style="color: black;"></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: 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"><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: 12pt; font-family: Symbol;"><span
style=""><span style="font: 7pt "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: 0.0001pt;
line-height: normal;"><span style="font-size: 12pt;
font-family: "Times New
Roman","serif";"></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: 12pt; font-family: "Times New
Roman","serif";"><span style="color:
red;"></span></span>
<p class="MsoNormal" style="margin-bottom: 0.0001pt;
line-height: normal;">
</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>
</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:
0.0001pt; text-indent: -18pt; line-height: normal;"><span
style="font-size: 12pt; font-family: Symbol;"><span
style="">·<span style="font: 7pt "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: 12pt; line-height: 115%; font-family:
"Times New Roman","serif";"><span
style=""> </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
moz-do-not-send="true" 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: 0.0001pt;
line-height: normal;"><span style="font-size: 12pt;
font-family: "Times New
Roman","serif"; color: black;"> <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: 12pt; font-family: "Times New
Roman","serif"; color: black;"></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"> <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>
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<br>
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