<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:10pt"><div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:10pt"><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><font size="2" face="Tahoma">----- Forwarded Message ----<br><b><span style="font-weight: bold;">From:</span></b> P.R.Anand Narayanan <nandu_cooldevil@yahoo.co.in><br><b><span style="font-weight: bold;">To:</span></b> gromacs <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Mon, 18 January, 2010 12:12:45 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re:Re: Polymer-protein<br></font><br><div style="font-family:times new roman, new york, times, serif;font-size:12pt;"><div><div>Dear Gromacs users,</div><div><br></div><div>I have to attach a
chemical polymer to a protein and when I created peptide bonds and
saved it, the entire format of the pdb file changed. That is the entire
identity of the protein was lost and the pdb file was saved in the form
of ATOMS and not residues.<br>That is,<br>"PROTEIN IN ITS PDB FORMAT"-<br>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>1<span style=""> </span>N<span style=""> </span>GLY
A<span style=""> </span>3<span style="">
</span>13.102<span style=""> </span>19.500<span style=""> </span>65.823<span style="">
</span>1.00 35.46<span style=""> </span>N<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>2<span style=""> </span>CA<span style=""> </span>GLY
A<span style=""> </span>3<span style="">
</span>13.351<span style=""> </span>19.610<span style=""> </span>64.358<span style="">
</span>1.00 35.46<span style=""> </span>C<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>3<span style=""> </span>C<span style=""> </span>GLY
A<span style=""> </span>3<span style="">
</span>13.672<span style=""> </span>18.235<span style=""> </span>63.779<span style="">
</span>1.00 35.46<span style=""> </span>C<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>4<span style=""> </span>O<span style=""> </span>GLY
A<span style=""> </span>3<span style="">
</span>12.833<span style=""> </span>17.341<span style=""> </span>64.029<span style="">
</span>1.00 35.46<span style=""> </span>O<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>5<span style=""> </span>N<span style=""> </span>ILE
A<span style=""> </span>4<span style="">
</span>14.789<span style=""> </span>18.041<span style=""> </span>63.100<span style="">
</span>1.00 33.26<span style=""> </span>N<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>6<span style=""> </span>CA<span style=""> </span>ILE
A<span style=""> </span>4<span style="">
</span>15.065<span style=""> </span>16.703<span style=""> </span>62.567<span style="">
</span>1.00 33.26<span style=""> </span>C<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>7<span style=""> </span>C<span style=""> </span>ILE
A<span style=""> </span>4<span style="">
</span>14.891<span style=""> </span>15.581<span style=""> </span>63.573<span style="">
</span>1.00 33.26<span style=""> </span>C<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>8<span style=""> </span>O<span style=""> </span>ILE
A<span style=""> </span>4<span style="">
</span>14.301<span style=""> </span>14.552<span style=""> </span>63.227<span style="">
</span>1.00 33.26<span style=""> </span>O<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>9<span style=""> </span>CB<span style=""> </span>ILE
A<span style=""> </span>4<span style="">
</span>16.488<span style=""> </span>16.599<span style=""> </span>61.907<span style="">
</span>1.00 29.15<span style=""> </span>C<span style=""> </span></font></p>
<p class="MsoPlainText"><font size="2">ATOM<span style=""> </span>10<span style=""> </span>CG1 ILE A<span style="">
</span>4<span style=""> </span>16.757<span style=""> </span>15.146<span style="">
</span>61.417<span style=""> </span>1.00 29.15<span style=""> </span>C<span style="">
</span></font></p>
<p class="MsoPlainText"><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 13px;"><span class="Apple-style-span" style="font-size: small;"><br></span></span></font></p><span style="font-size:10pt;"><span style="">AFTER BINDING THE POLYMER TO IT, THE PDB IS NOW SAVED AS:<br><span class="Apple-style-span" style="font-size: 16px; ">HETATM<span style=""> </span>1<span style=""> </span>N<span style="">
</span>1<span style=""> </span>-24.998<span style=""> </span>12.703<span style="">
</span>12.925</span><br></span></span>
<p class="MsoPlainText">HETATM<span style=""> </span>2<span style=""> </span>C<span style="">
</span>2<span style=""> </span>-24.749<span style=""> </span>12.813<span style="">
</span>11.460</p>
<p class="MsoPlainText">HETATM<span style=""> </span>3<span style=""> </span>C<span style="">
</span>3<span style=""> </span>-24.428<span style=""> </span>11.438<span style="">
</span>10.881</p>
<p class="MsoPlainText">HETATM<span style=""> </span>4<span style=""> </span>O<span style="">
</span>4<span style=""> </span>-25.267<span style=""> </span>10.544<span style="">
</span>11.131</p>
<p class="MsoPlainText">HETATM<span style=""> </span>5<span style=""> </span>H<span style="">
</span>5<span style=""> </span>-25.225<span style=""> </span>13.528<span style="">
</span>13.462</p>
<p class="MsoPlainText">HETATM<span style=""> </span>6<span style=""> </span>H<span style="">
</span>6<span style=""> </span>-25.636<span style=""> </span>13.216<span style="">
</span>10.970</p>
<p class="MsoPlainText">HETATM<span style=""> </span>7<span style=""> </span>H<span style="">
</span>7<span style=""> </span>-23.903<span style=""> </span>13.478<span style="">
</span>11.291</p>
<p class="MsoPlainText">HETATM<span style=""> </span>8<span style=""> </span>H<span style="">
</span>8<span style=""> </span>-24.228<span style=""> </span>12.218<span style="">
</span>13.362</p>
<p class="MsoPlainText">HETATM<span style=""> </span>9<span style=""> </span>H<span style="">
</span>9<span style=""> </span>-25.871<span style=""> </span>12.195<span style="">
</span>12.948</p>
<p class="MsoPlainText">HETATM<span style=""> </span>10<span style=""> </span>N<span style="">
</span>10<span style=""> </span>-23.311<span style=""> </span>11.244<span style="">
</span>10.202</p>
<p class="MsoPlainText"><span class="Apple-style-span" style="font-size: 13px; "> </span></p></div><div>That is, it is saved as single atoms and not as RESIDUES and hence the entire protein identity is lost. Are there any solutions to this or can I Use the same in gromacs??????? If yes, how can I use it in the pdb2gmx command????</div><div><br></div><div>Please help,</div><div>Thanking you,</div><div>regards,</div><div>Anand</div></div>
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