Hi Irene,
I simulated systems that contain MgATP too and performed MMPBSA calculations. Initially I had the same problem as yours because, as Jason pointed out, I forgot to use the strip_mask in my input file. Thus, I think that this is your problem too. It is also probably not bad idea to define manually your receptor and ligand in that case.
I had the similar problem with the structural waters that I kept during my simulations, but was not able to solve it. Anyway, this is another topic..:)
Regards,
Filip
--- On Tue, 8/9/11, Irene Newhouse <einew.hotmail.com> wrote:
> From: Irene Newhouse <einew.hotmail.com>
> Subject: Re: [AMBER] GBSA calculations with MgATP ligand
> To: amber.ambermd.org
> Date: Tuesday, August 9, 2011, 11:58 PM
>
> Ah ha! Thank you! I'll explore that in the manual - but I
> may have more questions later.
>
> Irene
>
> > Date: Tue, 9 Aug 2011 16:16:53 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] GBSA calculations with MgATP
> ligand
> >
> > Hi Irene,
> >
> > By default, MMPBSA.py will strip out all known ions
> and water molecules (if
> > strip_mdcrd=1, which is default). If you want to
> keep the Mg ion, then you
> > have to define a specific strip_mask in your input
> file.
> >
> > This may be what is causing your issues...
> >
> > HTH,
> > Jason
> >
> > On Tue, Aug 9, 2011 at 3:47 PM, Irene Newhouse <einew.hotmail.com>
> wrote:
> >
> > >
> > > Last week I was advised that my error messages
> from MMGBSA ...'cound not
> > > predict number of frames'... probably meant that
> something went wrong in
> > > parsing the overall trajectory into its
> constituents & I should look at the
> > > mdcrd files to verify that. I did & that's
> right, the molecules are messed
> > > up.
> > >
> > > When I originally prepared the inputs, I did not
> write receptor, ligand,
> > > complex w/out water & I had been doing those
> retroactively for the other
> > > systems in the series I'm currently studying - a
> set of several ligands
> > > bound to the same protein - and those had all
> worked properly, leading me to
> > > suspect the Mg is the issue. But to rule that
> out, I re-constituted the
> > > system, saving all the files I thought I needed
> right from the start, and
> > > reran the MD. Those results are now in, & I'm
> still having the same problem,
> > > so it looks like the Mg is the issue. These
> are the commands I issue to
> > > tleap:
> > >
> > > source leaprc.gaff
> > > source leaprc.ff99SB
> > > loadAmberPrep atp.prepi
> > > lig = loadAmberParams atp.frcmod
> > > pl = loadpdb mapr.pdb
> > > p = loadpdb ns.pdb
> > > l = loadpdb lig.pdb
> > > saveAmberParm l mgatp.prmtop mgatp.inpcrd
> > > saveAmberParm p ns.prmtop ns.inpcrd
> > > saveAmberParm pl mgatpprnw.prmtop
> mgatpprnw.inpcrd
> > > solvateBox pl TIP3PBOX 12.0
> > > addions pl Na+ 0
> > > addions pl Na+ 25 Cl- 25
> > > saveAmberParm pl mgatppr.prmtop mgatppr.inpcrd
> > >
> > > where atp.prepi & atp.frcmod are for ATP,
> from a web site referenced
> > > threads on this mailer's archive:
> > > http://www.pharmacy.manchester.ac.uk/bryce/amber#org,
> pl is a pdb
> > > containing the protein, plus ATP oriented as
> desired, as a residue, & Mg as
> > > another residue, also with the desired
> coordinates. Ns.pdb is the protein
> > > alone. l is a pdb file containing ATP &
> Mg, which I simply edited from pl.
> > > For input into MMPBSA.py, -sp is
> mgatppr.prmtop, -cp is mgatpprnw.prmtop,
> > > -rp is ns.prmtop & -lp is mgatp.prmtop...
> > >
> > > I would have preferred to define MgATP as a
> single unit, but antechamber
> > > was unable to process the Mg.
> > >
> > > Can someone tell me how [or if] I can calculate
> the free energy of MgATP
> > > binding to this protein? If it involves yet
> another way to set the system up
> > > & a third simulation, so be it.
> > >
> > > Thanks!
> > > Irene Newhouse
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
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Received on Tue Aug 09 2011 - 19:30:03 PDT
