Le 21/09/2010 13:37, case a écrit :
> 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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Thanks David, I have just compared the coordinates in the two files and
they are identical. I have loaded the Trpcage prmtop and inpcrd files
and I have a distorded structure too. Indeed, the problem should be the
display in VMD. I use VMD 1.8.6 and load the files using the VMD main
menu: File>new molecule>*.prmtop (amber7 parm) and load and then I load
for this prmtop file, the corresponding inpcrd file (as indicated in the
tutorial).
Even if the molecule seems good on a graphic display is it recommended
to look carefully at the prepin file to check the atom type etc... ?
So, the positive total energy (~ 5.0 10+1) observe after the
minimization could be related to the wrong parametrization of the gaff
forcefield for this type of molecule? (with non classical peptidic bond
but CO-NH-NH-C (side chain)-CO-NH-NH-...). Thanks
Best wishes,
Baptiste
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Received on Tue Sep 21 2010 - 06:30:04 PDT
