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</o:shapelayout></xml><![endif]--></head><body lang=ZH-CN link=blue vlink=purple style='text-justify-trim:punctuation'><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Hello, I’ve got a pdb file,but while I convert it to gro files, I met such problem:<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><i><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms<o:p></o:p></span></i></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>I find that in the rtp files of the ff files, the H atom linked with C-alpha is called H, but in the pdb file, the same hydrogen atom is called HA, I think this may be the problem. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>So, my problem is, how to convert my pdb files to make the atom names consistent between the pdb and rtp files?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>KONG Xian<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Tsinghua University, Beijing, China<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif"'>2011/9/13<o:p></o:p></span></p></div> <BR><BR>__________ Information from ESET NOD32 Antivirus, version of virus signature database 6458 (20110912) __________<BR><BR>The message was checked by ESET NOD32 Antivirus.<BR><BR><A HREF="http://www.eset.com">http://www.eset.com</A><BR> </body></html>