By default, MMPBSA.py strips out all water and ions from the trajectory
file (default strip_mask=“:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+"). I
assume that some of your ions that are in your receptor (and possibly
ligand) prmtop are being stripped out by MMPBSA.py and thus your receptor
prmtop does not match the receptor trajectory file created by MMPBSA.py.
This kind of inconsistency would lead to the "nan" values you are seeing in
the results file. In this case, you should specify strip_mask explicitly in
your MMPBSA.py input to strip the correct residues, so as to keep all ions
that you want to consider with your MM-PBSA calculation.
I hope that helps.
-Bill
On Tue, May 22, 2012 at 6:54 PM, Alejandro Blanco <ablancomu.gmail.com>wrote:
> Hi Amber users.
> I've a crystallographic structure that involve an homodimeric enzyme, where
> each monomer have two molecules of MgATP binding to it, one of this
> correspond to the phosphoryl donor (MgATP catalytic) and the other one acts
> as inhibithor of the enzymatic activity (MgATP allosteric). Also, each
> monomer has an ion site near the two binding sites for MgATP. Kinetic
> studies has revealed that pottasium bound to this site increases the
> affinity for MgATP allosteric and the enzymatic inhibition. So, I'm
> interested in calculate the binding energy for MgATP allosteric with and
> without potassium bound to the ion site, using the method MM-PBSA, with one
> minimized structure with explicit solvent, as described in this paper "J
> Comput Chem 31: 797-810, 2010".
> The prmtop file for the complex has the enzyme, with the four MgATP and the
> two potassium ions.
> The prmtop file of the receptor has the enzyme with the two MgATP catalytic
> and thw two pottasium.
> The prmtop file for the ligand has the two MgATP allosteric.
> I only include the crystallographic waters in the files for the
> minimization, also this file include the counter ions for neutralization.
> I only use the last frame of the trajectory file (minimization.mdcrd) for
> the calculations.
> When I run MM-PBSA (MMPBSA.py) in amber11, the output file has no values of
> binding free energy. This is the output file:
>
> | Run on vie may 18 16:07:09 CLT 2012
>
> |Input file:
> |--------------------------------------------------------------
> |Input file for running PB and GB in serial
> |&general
> | keep_files=2, startframe=50,
> |/
> |&pb
> | istrng=0.150,
> |/
> |&decomp
> | idecomp=2, dec_verbose=3,
> |/
> |--------------------------------------------------------------
> |Solvated complex topology file: ./toppar/complex_solvated-ions.prmtop
> |Complex topology file: ./toppar/complex-nowt.prmtop
> |Receptor topology file: ./toppar/receptor.prmtop
> |Ligand topology file: ./toppar/ligando.prmtop
> |Initial mdcrd(s): minimization.mdcrd
> |
> |Best guess for receptor mask: ":1-620:623-628"
> |Best guess for ligand mask: ":621-622"
>
> |Calculations performed using 2 frames.
> |Poisson Boltzmann calculations performed using internal PBSA solver in
> sander.
> |
> |All units are reported in kcal/mole.
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> POISSON BOLTZMANN:
>
> Complex:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -4162.0960 0.0000
> 0.0000
> EEL -34496.7736 0.0000
> 0.0000
> EPB -14316.2634 0.0000
> 0.0000
> ECAVITY 138.1355 0.0000
> 0.0000
>
> G gas -38658.8696 0.0000
> 0.0000
> G solv -14178.1279 0.0000
> 0.0000
>
> TOTAL -52836.9975 0.0000
> 0.0000
>
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS nan nan
> nan
> EEL inf nan
> nan
> EPB -12535.4077 0.0000
> 0.0000
> ECAVITY 136.7652 0.0000
> 0.0000
>
> G gas nan nan
> nan
> G solv -12398.6425 0.0000
> 0.0000
>
> TOTAL nan nan
> nan
>
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -14.6917 0.0000
> 0.0000
> EEL 2097.2930 0.0000
> 0.0000
> EPB -1720.7177 0.0000
> 0.0000
> ECAVITY 5.8754 0.0000
> 0.0000
>
> G gas 2082.6013 0.0000
> 0.0000
> G solv -1714.8423 0.0000
> 0.0000
>
> TOTAL 367.7590 0.0000
> 0.0000
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> VDWAALS nan nan
> nan
> EEL -inf nan
> nan
> EPB -60.1380 0.0000
> 0.0000
> ECAVITY -4.5051 0.0000
> 0.0000
>
> DELTA G gas nan nan
> nan
> DELTA G solv -64.6431 0.0000
> 0.0000
>
>
> DELTA G binding = nan +/- nan
> nan
>
>
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> Can anyone tell me what i'm doing wrong? or some suggestion?
>
> Thanks in advance.
>
> Alejandro Blanco
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 22 2012 - 18:30:03 PDT
