Hi,
I can't seem to find the tutorial you're referencing (or I can't find the proper vmd section) so I'm not sure how the tutorial told you to load the inpcrd... but inpcrds will appear correctly if you display them is as amber restart files. Does using this setting help any?
Trevor
________________________________________
From: Baptiste Legrand [bap.legrand.gmail.com]
Sent: Tuesday, September 21, 2010 6:12 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Creation of a mol2/pdb initial structure file of a pharmaceutical compound.
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 Wed Sep 22 2010 - 01:00:04 PDT
