Hi Karl,
Thanks for you interest. I have used unique key words to manually control
the FF parameters, in way to ensure that I am using the best matching FF
parameter from the GAFF library. I have attached the PREP and FRCMOD file
for your reference.
Thanks and regards
Aneesh
On Thu, Jan 31, 2013 at 2:40 PM, Karl N. Kirschner <
kkirsch.scai.fraunhofer.de> wrote:
> Hello Aneesh,
>
> I have been thinking about your problem some, and I am curious about the
> performance of the parameters within your ligand. Could you send an image
> of your molecule with the atom type definition labeled next to the
> corresponding atom? (I assume you used parmchk after running antechamber to
> supply any missing parameters, correct?).
>
> Cheers,
> Karl
>
> ----- Original Message -----
> From: "aneesh cna" <aneeshcna.gmail.com>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Wednesday, January 30, 2013 8:22:33 AM
> Subject: Re: [AMBER] Fwd: Regarding the problem with ligand conformation
>
> I maintain the system tepmerature at 300K. As Karl suggested, to see there
> is any effect of temperature on ligand conformation, I would like to try
> out few simulations possibly in the range of 283K - 293K.
>
> On Wed, Jan 30, 2013 at 11:31 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > > 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 Thu Jan 31 2013 - 04:00:02 PST
