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)
>
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>
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>
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Received on Fri Apr 01 2016 - 13:30:04 PDT
