<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><font class="Apple-style-span" face="arial, helvetica, sans-serif">Dear Sir,</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">I energy optimised the polymer-protein structure using HYPERCHEM. The moment I created peptide bonds between them, the pdb was saved like the format mentioned previously. for eg;</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">HETATM 1 N 1 -24.998 12.703 12.925<br>> <br>> HETATM 2 C 2 -24.749 12.813 11.460<br>> <br>> HETATM
3 C 3 -24.428 11.438 10.881<br>> <br>> HETATM 4 O 4 -25.267 10.544 11.131<br>> <br>> HETATM 5 H 5 -25.225 13.528 13.462<br>> <br>> HETATM 6 H 6 -25.636 13.216 10.970<br>> <br>> HETATM 7 H 7 -23.903 13.478 11.291<br><br></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">So, if there is NO other way of using this type of pdb file in GROMACS; can you please suggest any other software where I can successfully make covalent bonds between the protein and polymer, optimise them under force-field algorithms
and THEN use the pdb file in GROMACS? </font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">Eagerly awaiting your advise and reply!!!</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><span class="Apple-style-span" style="font-family: arial, helvetica, sans-serif; ">>>>"What program did you use to create this new PDB file? It looks like it severely <br>crippled the file, changing just about everything about it. There is certainly <br>no way to use this .pdb file, since there aren't even any residue names defined <br>in it.<br><br>-Justin"</span></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><<<<</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif"><br></font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">Thanking
you, </font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">Regards,</font></div><div><font class="Apple-style-span" face="arial, helvetica, sans-serif">Anand</font></div><div style="position:fixed"></div>
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