<p class="MsoNormal"><span style="font-size:12.0pt;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:12.0pt;line-height:115%;font-family:
"Times New Roman","serif"">I created a lipopeptide (lauroic acid <span style="mso-spacerun:yes"> </span>connected to an 8-residue peptide which starts
with Valine).</span></p>
<p class="MsoListParagraphCxSpFirst" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><span style="font-size:12.0pt;line-height:115%;font-family:Symbol;mso-fareast-font-family:
Symbol;mso-bidi-font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><span style="font-size:12.0pt;line-height:115%;
font-family:"Times New Roman","serif"">If I try to use pdb2gmx with -ter
flag<span style="mso-spacerun:yes"> </span>(Start terminus VAL-2: None, End
terminus ASP-9: COO-), everything seems to work (topology is created.).</span></p>
<p class="MsoListParagraphCxSpMiddle" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1"><span style="font-size:12.0pt;line-height:115%;font-family:Symbol;mso-fareast-font-family:
Symbol;mso-bidi-font-family:Symbol"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><span style="font-size:12.0pt;line-height:115%;
font-family:"Times New Roman","serif"">But, if I try to use pdb2gmx with -ter
flag<span style="mso-spacerun:yes"> </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:12.0pt;line-height:
115%;font-family:"Times New Roman","serif""> <b>Fatal error: Atom N not found in residue <a 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><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:9.0pt;line-height:115%;font-family:
"Times New Roman","serif"">GROMACS molecule input test</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif"">574</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CA<span style="mso-spacerun:yes">
</span>1<span style="mso-spacerun:yes"> </span>11.027<span style="mso-spacerun:yes"> </span>5.295<span style="mso-spacerun:yes">
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CB<span style="mso-spacerun:yes">
</span>2<span style="mso-spacerun:yes"> </span>10.894<span style="mso-spacerun:yes"> </span>5.299<span style="mso-spacerun:yes">
</span>3.078</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CG<span style="mso-spacerun:yes">
</span>3<span style="mso-spacerun:yes"> </span>10.777<span style="mso-spacerun:yes"> </span>5.234<span style="mso-spacerun:yes">
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CD<span style="mso-spacerun:yes">
</span>4<span style="mso-spacerun:yes"> </span>10.645<span style="mso-spacerun:yes"> </span>5.254<span style="mso-spacerun:yes">
</span>3.078</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CE<span style="mso-spacerun:yes">
</span>5<span style="mso-spacerun:yes"> </span>10.521<span style="mso-spacerun:yes"> </span>5.203<span style="mso-spacerun:yes">
</span>3.153</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CZ<span style="mso-spacerun:yes">
</span>6<span style="mso-spacerun:yes"> </span>10.392<span style="mso-spacerun:yes"> </span>5.251<span style="mso-spacerun:yes">
</span>3.086</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CM<span style="mso-spacerun:yes">
</span>7<span style="mso-spacerun:yes"> </span>10.266<span style="mso-spacerun:yes"> </span>5.207<span style="mso-spacerun:yes">
</span>3.161</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CN<span style="mso-spacerun:yes">
</span>8<span style="mso-spacerun:yes"> </span>10.140<span style="mso-spacerun:yes"> </span>5.272<span style="mso-spacerun:yes">
</span>3.103</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CO<span style="mso-spacerun:yes">
</span>9<span style="mso-spacerun:yes"> </span>10.014<span style="mso-spacerun:yes"> </span>5.221<span style="mso-spacerun:yes">
</span>3.172</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CP<span style="mso-spacerun:yes">
</span>10<span style="mso-spacerun:yes"> </span>9.885<span style="mso-spacerun:yes"> </span>5.279<span style="mso-spacerun:yes">
</span>3.112</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>CQ<span style="mso-spacerun:yes">
</span>11<span style="mso-spacerun:yes"> </span>9.761<span style="mso-spacerun:yes"> </span>5.203<span style="mso-spacerun:yes">
</span>3.160</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes">
</span>C<span style="mso-spacerun:yes"> </span>12<span style="mso-spacerun:yes"> </span>11.101<span style="mso-spacerun:yes">
</span>5.430<span style="mso-spacerun:yes"> </span>3.147</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>1DPP<span style="mso-spacerun:yes"> </span>O<span style="mso-spacerun:yes">
</span>13<span style="mso-spacerun:yes"> </span>11.032<span style="mso-spacerun:yes"> </span>5.531<span style="mso-spacerun:yes">
</span>3.136</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>N<span style="mso-spacerun:yes">
</span>14<span style="mso-spacerun:yes"> </span>11.235<span style="mso-spacerun:yes"> </span>5.450<span style="mso-spacerun:yes">
</span>3.160</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>H<span style="mso-spacerun:yes">
</span>15<span style="mso-spacerun:yes"> </span>11.249<span style="mso-spacerun:yes"> </span>5.550<span style="mso-spacerun:yes">
</span>3.159</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>CA<span style="mso-spacerun:yes">
</span>16<span style="mso-spacerun:yes"> </span>11.368<span style="mso-spacerun:yes"> </span>5.385<span style="mso-spacerun:yes">
</span>3.181</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>CB<span style="mso-spacerun:yes">
</span>17<span style="mso-spacerun:yes"> </span>11.390<span style="mso-spacerun:yes"> </span>5.233<span style="mso-spacerun:yes">
</span>3.181</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>CG1<span style="mso-spacerun:yes">
</span>18<span style="mso-spacerun:yes"> </span>11.332<span style="mso-spacerun:yes"> </span>5.172<span style="mso-spacerun:yes">
</span>3.308</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>CG2<span style="mso-spacerun:yes">
</span>19<span style="mso-spacerun:yes"> </span>11.338<span style="mso-spacerun:yes"> </span>5.161<span style="mso-spacerun:yes">
</span>3.056</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>C<span style="mso-spacerun:yes">
</span>20<span style="mso-spacerun:yes"> </span>11.486<span style="mso-spacerun:yes"> </span>5.449<span style="mso-spacerun:yes">
</span>3.103</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>2VAL<span style="mso-spacerun:yes"> </span>O<span style="mso-spacerun:yes">
</span>21<span style="mso-spacerun:yes"> </span>11.498<span style="mso-spacerun:yes"> </span>5.436<span style="mso-spacerun:yes">
</span>2.982</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>…………..</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>63ASP<span style="mso-spacerun:yes"> </span>OD1<span style="mso-spacerun:yes">
</span>570<span style="mso-spacerun:yes"> </span>-0.306<span style="mso-spacerun:yes"> </span>14.874<span style="mso-spacerun:yes">
</span>3.343</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>63ASP<span style="mso-spacerun:yes"> </span>OD2<span style="mso-spacerun:yes">
</span>571<span style="mso-spacerun:yes"> </span>-0.451<span style="mso-spacerun:yes"> </span>15.030<span style="mso-spacerun:yes">
</span>3.289</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>63ASP<span style="mso-spacerun:yes"> </span>C<span style="mso-spacerun:yes">
</span>572<span style="mso-spacerun:yes"> </span>-0.057<span style="mso-spacerun:yes"> </span>15.023<span style="mso-spacerun:yes">
</span>3.106</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>63ASP<span style="mso-spacerun:yes"> </span>O1<span style="mso-spacerun:yes">
</span>573<span style="mso-spacerun:yes"> </span>0.014<span style="mso-spacerun:yes"> </span>15.003<span style="mso-spacerun:yes">
</span>3.207</span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;line-height:115%;font-family:
"Times New Roman","serif""><span style="mso-spacerun:yes"> </span>63ASP<span style="mso-spacerun:yes"> </span>O2<span style="mso-spacerun:yes">
</span>574<span style="mso-spacerun:yes"> </span>-0.029<span style="mso-spacerun:yes"> </span>15.104<span style="mso-spacerun:yes">
</span>3.017</span></p>
<p class="MsoNormal"><span style="font-size: 9pt; line-height: 115%; font-family: "Times New Roman","serif";"><span style="mso-spacerun:yes">
</span>16.23937<span style="mso-spacerun:yes"> </span>16.23937<span style="mso-spacerun:yes"> </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:12.0pt;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:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:TR">Any help will be appreciated.</span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:TR"> </span><span style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:TR">Thanks in advance</span>
</p><p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt"><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>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:
normal;tab-stops:45.8pt 91.6pt 137.4pt 183.2pt 229.0pt 274.8pt 320.6pt 366.4pt 412.2pt 458.0pt 503.8pt 549.6pt 595.4pt 641.2pt 687.0pt 732.8pt"><span style="font-size:12.0pt;font-family:"Times New Roman","serif";mso-fareast-font-family:
"Times New Roman";mso-fareast-language:TR">Deniz</span></p>