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dear Xian,<BR>
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open the PDB using text editor and replace the name...<BR>
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good luck<BR> <BR>
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From: xianshine@gmail.com<BR>To: gmx-users@gromacs.org<BR>Date: Tue, 13 Sep 2011 15:36:41 +0800<BR>Subject: [gmx-users] how to handle different atom names between pdb and rtp files.<BR><BR>
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<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>Hello, I’ve got a pdb file,but while I convert it to gro files, I met such problem:</SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US> </SPAN></P>
<P class=ecxMsoNormal><I><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while sorting atoms</SPAN></I></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US> </SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>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. </SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US> </SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>So, my problem is, how to convert my pdb files to make the atom names consistent between the pdb and rtp files?</SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US> </SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US> </SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>KONG Xian</SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>Tsinghua University, Beijing, China</SPAN></P>
<P class=ecxMsoNormal><SPAN style="FONT-FAMILY: 'Times New Roman','serif'; FONT-SIZE: 12pt" lang=EN-US>2011/9/13</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/" target=_blank>http://www.eset.com</A><BR><BR>-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</DIV> </div></body>
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