> what
> could be the lowest possible temperature where I can do a classical MD
> simulation?
What would be your ideal?
Bill
aneesh cna <aneeshcna.gmail.com> wrote:
> Hi Karl,
>
> Thanks for the reply. Since testing the fitness of each force-field terms
> will be time consuming, I fee it could be better to check the role of
> temperature on ligand conformation before getting into those QM-MM
> calculations. Looking from this aspect, I have a quick query that what
> could be the lowest possible temperature where I can do a classical MD
> simulation?
>
>
> Thanks in advance
>
>
> Regards,
> Aneesh
>
>
> On Tue, Jan 29, 2013 at 9:29 PM, Karl N. Kirschner <
> kkirsch.scai.fraunhofer.de> wrote:
>
> > Hi Aneesh,
> >
> > It is difficult to say if your simulations went wrong or not. For one,
> > maybe your ligand is sampling conformations that are appropriate for a room
> > temperature solution-phase model (assuming that is what you are doing). The
> > crystal structure was likely solved at a much lower temperature, resulting
> > in the preferred conformation you see in the PDB file.
> >
> > With that said, one could investigate how well the different force-field
> > terms that you are using perform at reproducing known experimental
> > observables in analogues, if available. Alternatively you could see how
> > they reproduce QM-generated rotational curves for that molecule or a
> > smaller analogue. Doing so may provide you some confidence in their use in
> > MD simulations. (Be forewarned, this can be time consuming to accomplish.)
> >
> > Best regards,
> > Karl
> >
> > ----- Original Message -----
> > From: "aneesh cna" <aneeshcna.gmail.com>
> > To: "AMBER Mailing List" <amber.ambermd.org>
> > Sent: Tuesday, January 29, 2013 2:12:38 PM
> > Subject: [AMBER] Fwd: Regarding the problem with ligand conformation
> >
> > Dear Amber users,
> >
> > I am working with the protein-ligand systems. The protein-ligand complex
> > structure was obtained from Protein Data Bank. Before starting the
> > simulation, I have carried out QM calculation ( b3lyp/6-311+g* ) of ligand
> > to get the optimized structure and ESP fitted point charge for the atoms.
> > The optimized ligand geometry was similar to the crystal structure. Then, I
> > have used the antechamber module of Amber to prepare the parameter file (
> > PREP and FRCMOD files) for the ligand, where I used the GAFF force field.
> >
> > Unfortunately, the ligand geometry has been changed drastically during the
> > initial stages of production run ( after ~1ns of equilibration phase) of
> > simulation. The ligand keep its proper conformation ( i.e. close to
> > crystal conformation) for the initial ~1 ns phase of equilibration. Is it a
> > problem with force field? . If so ( i.e., if there is any problem with
> > ligand FF parameters), the observed conformational changes should happen in
> > the initial stage of the simulation rather than at the end of ~1ns
> > equilibration.
> >
> >
> > Can anyone help me to figure out what went wrong with my simulation.
> >
> >
> > I have attached three snapshot of the ligand (crystal structure, QM
> > optimized, after equilibration respectively), for your reference.
> >
> >
> >
> > Thanks in advance
> >
> >
> > Sincerely
> > Aneesh
> >
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Received on Tue Jan 29 2013 - 22:30:03 PST
