Erik Marklund wrote:
On Tue, 2006-10-24 at 04:59 +1000, Mark Abraham wrote:
Qiao Baofu wrote:
Thanks. Now I understand what happens.
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?!!
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).
Well the URL I provided above omits PDB files from the list of file
types that VMD reads for bond connectivity. Hence I suspect Baofu has
misinterpreted something, or that manual section is incomplete.
Mark
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