On Tue, Aug 9, 2011 at 10:16 PM, filip fratev <filipfratev.yahoo.com> wrote:
> 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..:)
>
It is another topic, but I do have a solution. You need to post-process the
trajectories yourself so that they specifically keep the waters you want to
keep (the "closest" command may be helpful to you here, or you may have to
write a script to do it yourself).
After you've done this, you only need to supply a complex_prmtop,
receptor_prmtop, and ligand_prmtop (with the waters being in either the
receptor or ligand prmtop), and then set strip_mdcrd=0. This will prevent
MMPBSA.py from stripping any molecules from your system, including waters.
HTH,
Jason
> 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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> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 09 2011 - 20:00:04 PDT
