Thanks. Now I understand what happens.<br><br>But in the
user-manual of VMD, it is said that only four Gromacs file (GRO, G96,
XTC, TRR) and .pdb can be read by VMD. But only the .pdb contain the
information of bond-connectivity (if I understand correctly). The point
is that the output .pdb file from mdrun contains only the coordinate
information! How can I tell VMD the bond-connectivity information?!!
<br><br>I used the "mol new myfile.gro autobonds 0" to see my molecules. Unfortunately, only atoms are displayed, no connection. <br><br><br><div><span class="gmail_quote">2006/10/23, Ignacio Fernández Galván <
<a href="mailto:jellby@yahoo.com">jellby@yahoo.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">--- Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">
Mark.Abraham@anu.edu.au</a>> wrote:<br><br>> Right, so like I said earlier, you're not giving it your topology,<br>> because you're loading from a .gro file. Instead, VMD is making stuff<br>> up<br><br>Incidentally, you can disable this behaviour by loading the file in VMD
<br>with "mol new myfile.gro autobonds 0" (or something like that).<br><br>Send instant messages to your online friends <a href="http://uk.messenger.yahoo.com">http://uk.messenger.yahoo.com</a><br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies<br>Max-von-Laue-Str. 1<br>60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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