Yes. Gromacs can only generate the .pdb file without CONNECTION. I think it is not only Gromacs but Material Studio that do like that. For more than 2 molecules, the softwares give only the coordinate data. <br><br>I find a
top2psf.tcl file on the website of VMD (Script Library). It is said this script can transfer .top file to .psf file, which can be recognized by VMD. But I don't know how to use it and the website of VMD doesn't give the instrution how to use it. :(
<br><br><br><div><span class="gmail_quote">2006/10/24, Erik Marklund <<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
><br>> PDB files do not contain bond connectivity. By the look of<br>> <a href="http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html">http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html</a>, you can't
<br>> tell VMD your gromacs connectivity, unless you write your own plug-in to<br>> VMD (hint, hint). You could also try asking the VMD mailing list. Your<br>> simplest plan is likely to be to generate a PSF or PARM file with an
<br>> equivalent topology, for they are used in other MD codes to contain the<br>> connectivity.<br><br>That's not entirely true. Normally, pdb files do not contain topological<br>information, but they CAN do so through a CONNECT block. This is
<br>probably why VMD claims that ".pdb contain the information of bond-<br>connectivity" (don't use vmd myself, just cited Bafou above). However,<br>to my knowledge, gromacs completely ignores CONNECT blocks in pdb
<br>output/input, which is why you see atoms only, and no connection.<br></blockquote></div><br clear="all"><br>-- <br>Sincerely yours,<br>**********************************************<br>Baofu Qiao, PhD<br>Frankfurt Institute for Advanced Studies
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