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?!!
I used the "mol new myfile.gro autobonds 0" to see my molecules. Unfortunately, only atoms are displayed, no connection.
2006/10/23, Ignacio Fernández Galván <
[EMAIL PROTECTED]>:
--- Mark Abraham < [EMAIL PROTECTED]> wrote:
> Right, so like I said earlier, you're not giving it your topology,
> because you're loading from a .gro file. Instead, VMD is making stuff
> up
Incidentally, you can disable this behaviour by loading the file in VMD
with "mol new myfile.gro autobonds 0" (or something like that).
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Sincerely yours,
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Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
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