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On 1/07/2011 8:35 PM, Emine Deniz Tekin wrote:
<blockquote
cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
type="cite">
<p class="MsoNormal"><span style="font-size: 12pt; line-height:
115%; font-family: "Times New
Roman","serif";">Hi Gromacs users,</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height:
115%; font-family: "Times New
Roman","serif";"><br>
</span></p>
<p class="MsoNormal"><span style="font-size: 12pt; line-height:
115%; font-family: "Times New
Roman","serif";">I created a lipopeptide
(lauroic acid <span style=""> </span>connected to an
8-residue peptide which starts
with Valine).</span></p>
</blockquote>
<br>
How is the link from acid to peptide created?<br>
<br>
<blockquote
cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
type="cite">
<p class="MsoListParagraphCxSpFirst" style="text-indent: -18pt;"><span
style="font-size: 12pt; line-height: 115%; font-family:
Symbol;"><span style="">·<span style="font: 7pt "Times
New Roman";">
</span></span></span><span style="font-size: 12pt;
line-height: 115%; font-family: "Times New
Roman","serif";">If I try to use pdb2gmx with
-ter
flag<span style=""> </span>(Start terminus VAL-2: None, End
terminus ASP-9: COO-), everything seems to work (topology is
created.).</span></p>
</blockquote>
<br>
Does that topology work for MD? Why does pdb2gmx think there's 9
residues, and below there seem to be 63?<br>
<br>
<blockquote
cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
type="cite">
<p class="MsoListParagraphCxSpMiddle" style="text-indent: -18pt;"><span
style="font-size: 12pt; line-height: 115%; font-family:
Symbol;"><span style="">·<span style="font: 7pt "Times
New Roman";">
</span></span></span><span style="font-size: 12pt;
line-height: 115%; font-family: "Times New
Roman","serif";">But, if I try to use pdb2gmx
with -ter
flag<span style=""> </span>for more than one lipopeptide at
desired positions, it gives the following error. (again says
Start terminus
VAL-2: None, End terminus ASP-9: COO- )</span></p>
<p class="MsoListParagraphCxSpLast"><span style="font-size: 12pt;
line-height: 115%; font-family: "Times New
Roman","serif";"> <b>Fatal error: Atom N not
found in residue <a moz-do-not-send="true"
href="http://seq.nr">seq.nr</a>.
1 while adding improper</b></span></p>
<p class="MsoNormal"><span style="font-size: 12pt; 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></p>
</blockquote>
<br>
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.<br>
<br>
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 :)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTi=WnvvMrHLN07MhntAGc=1Pdirxpw@mail.gmail.com"
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 style=""> </span>1DPP<span
style=""> </span>CA<span style="">
</span>1<span style=""> </span>11.027<span style=""> </span>5.295<span
style="">
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CB<span style="">
</span>2<span style=""> </span>10.894<span style=""> </span>5.299<span
style="">
</span>3.078</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CG<span style="">
</span>3<span style=""> </span>10.777<span style=""> </span>5.234<span
style="">
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CD<span style="">
</span>4<span style=""> </span>10.645<span style=""> </span>5.254<span
style="">
</span>3.078</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CE<span style="">
</span>5<span style=""> </span>10.521<span style=""> </span>5.203<span
style="">
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CZ<span style="">
</span>6<span style=""> </span>10.392<span style=""> </span>5.251<span
style="">
</span>3.086</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CM<span style="">
</span>7<span style=""> </span>10.266<span style=""> </span>5.207<span
style="">
</span>3.161</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CN<span style="">
</span>8<span style=""> </span>10.140<span style=""> </span>5.272<span
style="">
</span>3.103</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CO<span style="">
</span>9<span style=""> </span>10.014<span style=""> </span>5.221<span
style="">
</span>3.172</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CP<span style="">
</span>10<span style=""> </span>9.885<span style=""> </span>5.279<span
style="">
</span>3.112</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>CQ<span style="">
</span>11<span style=""> </span>9.761<span style=""> </span>5.203<span
style="">
</span>3.160</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span><span
style=""> </span>1DPP<span style="">
</span>C<span style=""> </span>12<span style=""> </span>11.101<span
style="">
</span>5.430<span style=""> </span>3.147</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>1DPP<span
style=""> </span>O<span style="">
</span>13<span style=""> </span>11.032<span style=""> </span>5.531<span
style="">
</span>3.136</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>N<span style="">
</span>14<span style=""> </span>11.235<span style=""> </span>5.450<span
style="">
</span>3.160</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>H<span style="">
</span>15<span style=""> </span>11.249<span style=""> </span>5.550<span
style="">
</span>3.159</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>CA<span style="">
</span>16<span style=""> </span>11.368<span style=""> </span>5.385<span
style="">
</span>3.181</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>CB<span style="">
</span>17<span style=""> </span>11.390<span style=""> </span>5.233<span
style="">
</span>3.181</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>CG1<span style="">
</span>18<span style=""> </span>11.332<span style=""> </span>5.172<span
style="">
</span>3.308</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>CG2<span style="">
</span>19<span style=""> </span>11.338<span style=""> </span>5.161<span
style="">
</span>3.056</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>C<span style="">
</span>20<span style=""> </span>11.486<span style=""> </span>5.449<span
style="">
</span>3.103</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>2VAL<span
style=""> </span>O<span style="">
</span>21<span style=""> </span>11.498<span style=""> </span>5.436<span
style="">
</span>2.982</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>…………..</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>63ASP<span
style=""> </span>OD1<span style="">
</span>570<span style=""> </span>-0.306<span style=""> </span>14.874<span
style="">
</span>3.343</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>63ASP<span
style=""> </span>OD2<span style="">
</span>571<span style=""> </span>-0.451<span style=""> </span>15.030<span
style="">
</span>3.289</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>63ASP<span
style=""> </span>C<span style="">
</span>572<span style=""> </span>-0.057<span style=""> </span>15.023<span
style="">
</span>3.106</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>63ASP<span
style=""> </span>O1<span style="">
</span>573<span style=""> </span>0.014<span style=""> </span>15.003<span
style="">
</span>3.207</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style=""> </span>63ASP<span
style=""> </span>O2<span style="">
</span>574<span style=""> </span>-0.029<span style=""> </span>15.104<span
style="">
</span>3.017</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height:
115%; font-family: "Times New
Roman","serif";"><span style="">
</span>16.23937<span style=""> </span>16.23937<span
style=""> </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>
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