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. :(
2006/10/24, Erik Marklund <[EMAIL PROTECTED]>:
>
> PDB files do not contain bond connectivity. By the look of
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html, you can't
> tell VMD your gromacs connectivity, unless you write your own plug-in to
> VMD (hint, hint). You could also try asking the VMD mailing list. Your
> simplest plan is likely to be to generate a PSF or PARM file with an
> equivalent topology, for they are used in other MD codes to contain the
> connectivity.
That's not entirely true. Normally, pdb files do not contain topological
information, but they CAN do so through a CONNECT block. This is
probably why VMD claims that ".pdb contain the information of bond-
connectivity" (don't use vmd myself, just cited Bafou above). However,
to my knowledge, gromacs completely ignores CONNECT blocks in pdb
output/input, which is why you see atoms only, and no connection.
--
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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