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
>
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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 - 13:30:02 PDT
