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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 09 2011 - 14:00:04 PDT
