On Tue, Sep 21, 2010, Baptiste Legrand wrote:
>
> I have created mol2/pdb files of a chemical compound using Sirius. I
> have verified these files using vmd and save them. Then, according to
> the "sustiva" amber tutorial, leap was used to generate a prepin file
> and then prmtop and inpcrd files. When I look at the structure from the
> prepin file in xleap, the structure is good. Nevertheless, after saving
> the prmtop and the inpcrd files, the structure from these files is
> distorded in VMD. (Curiously if I generate a pdb file from these inpcrd
> and prmtop using the command ambpdb, the structure seems good in
> VMD...).
You don't give any details, but it sounds like you are not using the correct
VMD commands to load prmtop and inpcrd files into VMD. You can check to see
that the coordinates in the ambpdb-generated pdb (which is good) match those
in the inpcrd file.
...good luck....dac
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Received on Tue Sep 21 2010 - 05:00:03 PDT
