The bonds are defined by the topology file so them staying there really
doesn't mean anything. Is there a chance that you're not loading the
trajectory using the right format. For example if it was a periodic system
you have to use coordinates with box.
On Apr 1, 2016 4:28 PM, "Luke Presson" <luke.presson.centre.edu> wrote:
> The ligand was built using Chimera then further parameterized in
> antechamber with GAFF. I assumed that this created the desired parameters
> for the ligand.
>
> I see the ligand break apart when visualizing using VMD after I do a
> simulation and load the trajectory file (.mdcrd) and parameter file
> (.prmtop) into VMD. Basically what I mean by breaks apart is that the atoms
> of the ligand seem to move completely independently of each other but still
> maintain bonds. For example carbons in an aromatic ring might stretch to
> over ten angstroms away from each other because the atoms do not seem have
> anything holding them in a reasonable position relative to each other.
>
> ________________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Friday, April 1, 2016 3:40 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problems with periodic boundaries
>
> tleap builds the files, but it does not have parameters. ff99SB is for
> proteins and TIP3P is water. where did you get your ligand parameters? and
> what do you mean by "breaks apart"? please tell us exactly how you did this
> analysis - is this a visualization program? what files did you load into
> it? were they direct MD output, or processed somehow?
>
> On Fri, Apr 1, 2016 at 3:37 PM, Luke Presson <luke.presson.centre.edu>
> wrote:
>
> > The parameters were generated using tleap and the ff99SB force field and
> > solvated with a 12 angstrom box of TIP3PBOX water.
> >
> > ________________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Friday, April 1, 2016 1:51 PM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Problems with periodic boundaries
> >
> > On Fri, Apr 1, 2016 at 7:24 AM, Luke Presson <luke.presson.centre.edu>
> > wrote:
> > >
> > > I have been doing research modeling inhibitors of enzymes and have
> > recently run into a problem in which the ligand immediately breaks apart
> > once the simulation starts.
> >
> > This sounds like a problem with your parameters. How did you generate
> > parameters for this ligand?
> >
> > > When I have visualized the simulation it appears as though the atoms in
> > the ligand move independently but somehow maintain bonds even if they are
> > over 10 angstroms apart.
> >
> > Bond are never broken in a traditional MD simulation, so as long as
> > there is a bond defined in your topology that bond will appear in your
> > visualization program no matter how far apart the atoms in the bond
> > get.
> >
> > -Dan
> >
> > > This seems to be a more recent issue that I did not have while doing
> > this research in the past. I have been using periodic boundaries and
> > heating using NVT, then equilibrating with NPT. The one thing that I have
> > found that works is if I turn off periodic boundaries, however I would
> like
> > to be able to keep the system at constant pressure. I have not seen any
> > previous posts of this problem happening and am wondering if anyone has
> > some suggestions.
> > >
> > > Thanks,
> > > Luke Presson
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Apr 01 2016 - 14:00:03 PDT
