Re: [Apbs-users] pka-balanol example and MMPBSA

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Hi Elif --

I would recommend using the separate solvation energy (6 with automatic focusing, not 12) calculations for comparison.  It will also be more straightforward to manipulate the Coulombic interactions with this free energy cycle.

Use of force fields is a matter of personal choice.  While the charges should be the same as used for the MM part of the calculation, the radii do not have to be the same.

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnnl.gov/bios/baker.stm

> -----Original Message-----
> From: Elif Ozkirimli [mailto:eli...@bo...]
> Sent: Tuesday, May 31, 2011 1:57 AM
> To: Baker, Nathan
> Cc: apb...@li...; Keith Callenberg
> Subject: Re: [Apbs-users] pka-balanol example and MMPBSA
>
> Nathan,
>
> Thank you very much. I thought running apbs on the complex and on the
> components and then complex - ligand - protein ( as described in the
> pka-lig example) was sufficient to remove the self energies, no? If it
> does not then should my apbs input file have twelve calculations to
> make a free energy cycle:
>
> lig-coarse 2, 78
> lig-fine 2,78
> lig-coarse 2, 2
> lig-fine 2, 2
>
> protein-coarse 2,78
> protein-fine 2,78
> protein-coarse 2,2
> protein-fine 2, 2
>
> complex-coarse 2,78
> complex-fine 2, 78
> complex-coarse 2,2
> complex-fine 2,2
>
> energy = (complex-fine 2,78 - complex-fine 2,2) - (lig-fine 2,78 - lig-
> fine 2,2) - (protein-fine 2,78 - protein-fine 2,2)
>
> where 2 and 78 are the pdie and sdie, respectively.
>
>
> Another question is about the use of the same forcefield in the MD run
> and in the APBS calculations. In the MD run I used the Charmm
> forcefield, and therefore used Charmm in the pd2pqr and apbs runs as
> well. Is this reasonable?
>
> Thank you once again
> Elif.
>
>
>
>
>
>
> On May 31, 2011, at 5:38 AM, Baker, Nathan wrote:
>
> > Hello --
> >
> > The values of the PB-based solvation component are *very* sensitive
> > to several factors:  your choice of the molecular surface and
> > interface, your choice of the solute dielectric coefficient, and the
> > radii used for your calculation.  You should also be sure to include
> > only the solvation component to your energetics; perform a reference
> > calculation to remove your Coulombic terms (and self-energies) from
> > your solvation energy and then add the Coulombic terms back in with
> > your MM energies.
> >
> > Hope this helps,
> >
> > __________________________________________________
> > Nathan Baker
> > Pacific Northwest National Laboratory
> > Tel:  509-375-3997
> > http://kdi.pnnl.gov/bios/baker.stm
> >
> >
> >> -----Original Message-----
> >> From: Elif Ozkirimli [mailto:eli...@bo...]
> >> Sent: Thursday, May 26, 2011 6:32 AM
> >> To: Baker, Nathan
> >> Cc: Keith Callenberg; apb...@li...
> >> Subject: Re: [Apbs-users] pka-balanol example and MMPBSA
> >>
> >> Hello-
> >>
> >> Thanks for the quick response to my questions. I am trying to use
> >> apbs
> >> to find the binding energy between a protein and a peptide using the
> >> MMPBSA methodology. I have run a  simulation on the complex, I
> >> extract
> >> the protein and the peptide coordinates for each snapshot and run
> >> apbs
> >> to find the solvation contribution.
> >>
> >> When I run apbs-mol-surf.in as described in pka-lig example my PB
> >> value
> >> for a snapshot is around 25 kcal/mol (100 kJ/mol). Meanwhile, for the
> >> same snapshot, the electrostatic contribution from the MM part is
> >> around
> >> 130 kcal/mol (I do this calculation in VMD). Reading the
> >> literature, I
> >> have observed that the electrostatic contribution to solvation and
> >> to MM
> >> are usually the same order of magnitude.
> >>
> >> My questions are as follows:
> >>
> >> 1. Which input file is the most appropriate for my case? should I use
> >> vdW surface or molecular surface?
> >> 2. For MMPBSA; are the electrostatic contributions to solvation and
> >> nonbonded interaction energy always the same order of magnitude as
> >> reported in the literature? If you can share some insight and/or
> >> tips, I
> >> would appreciate it very much.
> >>
> >> Many thanks
> >>
> >> Elif.
> >>
> >>
> >>
> >>
> >>
> >> Baker, Nathan wrote:
> >>> Yes, the goal is to provide the finest mesh possible on the region
> >>> of
> >> interest:  the location of the ligand.
> >>>
> >>> Thanks,
> >>>
> >>> __________________________________________________
> >>> Nathan Baker
> >>> Pacific Northwest National Laboratory
> >>> Tel:  509-375-3997
> >>> http://kdi.pnnl.gov/bios/baker.stm
> >>>
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: Elif Ozkirimli [mailto:eli...@bo...]
> >>>> Sent: Wednesday, May 25, 2011 9:03 AM
> >>>> To: Keith Callenberg
> >>>> Cc: apb...@li...
> >>>> Subject: Re: [Apbs-users] pka-balanol example
> >>>>
> >>>> Here is another question:
> >>>>
> >>>> When I examine the input file  apbs-mol-surf.in, I notice that
> >>>> (for all
> >>>> three calculations on complex, on kinase and on ligand) the grid
> >>>> centering is performed on the complex in the coarse calculation
> >>>> and on
> >>>> the ligand in the fine calculation. Is there a specific reason for
> >> this?
> >>>>
> >>>> Thanks
> >>>> Elif.
> >>>>
> >>>>
> >>>> Elif Ozkirimli wrote:
> >>>>
> >>>>> Keith,
> >>>>>
> >>>>> Thanks for the quick response and for pointing out the examples
> >>>>> directory. I ran it and got the same results as in the README
> >>>>> file. (I
> >>>>> am running 1.2.1 due to some GLIBC problem with my computer.) In
> >>>>> any
> >>>>> case, I did not expect an order of magnitude difference which I
> >>>>> got
> >> for
> >>>>> the pka-balanol example.
> >>>>>
> >>>>> Here are two more questions:
> >>>>>
> >>>>> 1. When I run the pka-balanol example (or a similar input file
> >>>>> on my
> >> own
> >>>>> system) the final energy that is reported is not equal to
> >>>>> complex -
> >> pka
> >>>>> - balanol:
> >>>>>    For balanol:  Total electrostatic energy = 2.226791179892E+03
> >> kJ/mol
> >>>>> For pka: Total electrostatic energy = 1.827996136523E+05 kJ/mol
> >>>>> for complex: Total electrostatic energy = 1.850837986315E+05 kJ/
> >>>>> mol
> >>>>>
> >>>>> which does not add up to
> >>>>>
> >>>>> print energy 3 (complex) - 2 (pka) - 1 (bal) end
> >>>>>  Local net energy (PE 0) = 5.739379926058E+01 kJ/mol
> >>>>>  Global net ELEC energy = 5.739379926058E+01 kJ/mol
> >>>>>
> >>>>> Am I making a mistake here?
> >>>>>
> >>>>> 2. Should I do grid focusing as described in the pka-lig
> >>>>> directory?
> >>>>>
> >>>>> Thank you very much.
> >>>>> Elif
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> Keith Callenberg wrote:
> >>>>>
> >>>>>
> >>>>>> Hi Elif,
> >>>>>>
> >>>>>> Have you tried running the same example that is in the
> >>>>>> examples/pka-lig directory of APBS? It has been updated to
> >>>>>> include
> >>>>>> grid focusing.
> >>>>>>
> >>>>>> If so, do you get the values that are described in the readme
> >>>>>> file?
> >>>>>> http://apbs.svn.sourceforge.net/viewvc/apbs/trunk/examples/pka-
> >>>>>>
> >>>> lig/README.html?revision=1630
> >>>>
> >>>>>> You'll notice that there are different values for different
> >>>>>> versions
> >>>>>> of APBS (bugs have been fixed over time). What version of APBS
> >>>>>> are
> >> you
> >>>>>> running?
> >>>>>>
> >>>>>> Keith
> >>>>>>
> >>>>>> --
> >>>>>> Keith M. Callenberg
> >>>>>> Carnegie Mellon-University of Pittsburgh Program in Computational
> >>>>>>
> >>>> Biology
> >>>>
> >>>>>> kmc112@{pitt,cmu}.edu
> >>>>>> http://www.pitt.edu/~kmc112/
> >>>>>>
> >>>>>>
> >>>>>> On Wed, May 25, 2011 at 10:58 AM, Elif Ozkirimli
> >>>>>> <eli...@bo...> wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> Hi
> >>>>>>>
> >>>>>>> I tried to run the pka-balanol example from the apbs tutorial
> >>>>>>> (http://www.ics.uci.edu/~dock/manuals/apbs/html/tutorial/x307.html
> >>>>>>> ).
> >>>>>>>
> >>>> The
> >>>>
> >>>>>>> binding energy I find is:
> >>>>>>>
> >>>>>>> print energy 3 (complex) - 2 (pka) - 1 (bal) end
> >>>>>>> Local net energy (PE 0) = 5.739379926058E+01 kJ/mol
> >>>>>>> Global net ELEC energy = 5.739379926058E+01 kJ/mol
> >>>>>>>
> >>>>>>> which is an order of magnitude higher than what is stated on the
> >>>>>>> tutorial website (5.8 kJ/mol).
> >>>>>>>
> >>>>>>> I apologize if this issue has been addressed before, I
> >>>>>>> searched the
> >>>>>>>
> >>>> list
> >>>>
> >>>>>>> but could not find anything on the matter.
> >>>>>>>
> >>>>>>> I would appreciate it if you could tell me where my mistake is.
> >>>>>>>
> >>>>>>> Thanks
> >>>>>>> Elif.
> >>>>>>>
> >>>>>>> __________________
> >>>>>>> Elif Ozkirimli, PhD
> >>>>>>> Bogazici University
> >>>>>>> Chemical Engineering Department
> >>>>>>> Istanbul Turkey
> >>>>>>>
> >>>>>>>
> >>>>>>> The input file I am using is the following:
> >>>>>>>
> >>>>>>> read
> >>>>>>>   mol pqr bx6_7_lig_apbs.pqr  # Read balanol (mol 1)
> >>>>>>>   mol pqr bx6_7_apo_apbs.pqr  # Read PKA (mol 2)
> >>>>>>>   mol pqr bx6_7_bin_apbs.pqr  # Read complex (mol 3)
> >>>>>>> end
> >>>>>>> elec name bal
> >>>>>>>   mg-auto                          # Use the multigrid method
> >>>>>>>   dime 97 97 97                      # Grid dimensions
> >>>>>>>   fglen 70 70 70                      # Grid length
> >>>>>>>   fgcent mol 3                        # Center on complex
> >>>>>>>   cglen 80 80 80                      # Grid length
> >>>>>>>   cgcent mol 3                        # Center on complex
> >>>>>>>   mol 1
> >>>>>>>   lpbe
> >>>>>>>   bcfl sdh                           # Monopole boundary
> >>>>>>> conditions
> >>>>>>>   ion 1 0.000 2.0                    # Zero ionic strength
> >>>>>>>   ion -1 0.000 2.0
> >>>>>>>   pdie 2.0                           # Solute dielectric
> >>>>>>>   sdie 78.00                         # Solvent dielectric
> >>>>>>>   chgm spl0                          # Charge disc method
> >>>>>>> (linear)
> >>>>>>>   srfm smol                          # Smoothed molecular
> >>>>>>> surface
> >>>>>>>   srad 0.0                           # Solvent radius
> >>>>>>>   swin 0.3                           # Surface cubic spline
> >>>>>>> window
> >>>>>>>   sdens 10.0                         # Sphere density
> >>>>>>>   temp 298.15                        # Temperature
> >>>>>>>   gamma 0.105                        # Surface tension (in
> >>>>>>>
> >>>> kJ/mol/A^2)
> >>>>
> >>>>>>>   calcenergy total
> >>>>>>>   calcforce no
> >>>>>>>   write pot dx ligand                # Write potential to
> >>>>>>> ligand.dx
> >>>>>>> end
> >>>>>>> elec name pka
> >>>>>>>   mg-auto
> >>>>>>>   dime 97 97 97
> >>>>>>>   fglen 70 70 70
> >>>>>>>   fgcent mol 3
> >>>>>>>   cglen 80 80 80
> >>>>>>>   cgcent mol 3
> >>>>>>>   mol 2
> >>>>>>>   lpbe
> >>>>>>>   bcfl sdh
> >>>>>>>   ion 1 0.000 2.0
> >>>>>>>   ion -1 0.000 2.0
> >>>>>>>   pdie 2.0
> >>>>>>>   sdie 78.00
> >>>>>>>   chgm spl0
> >>>>>>>   srfm smol
> >>>>>>>   srad 0.0
> >>>>>>>   swin 0.3
> >>>>>>>   sdens 10.0
> >>>>>>>   temp 298.15
> >>>>>>>   gamma 0.105
> >>>>>>>   calcenergy total
> >>>>>>>   calcforce no
> >>>>>>>  write pot dx apo
> >>>>>>> end
> >>>>>>> elec name complex
> >>>>>>>   mg-auto
> >>>>>>>   dime 97 97 97
> >>>>>>>   fglen 70 70 70
> >>>>>>>   fgcent mol 3
> >>>>>>>   cglen 80 80 80
> >>>>>>>   cgcent mol 3
> >>>>>>>   mol 3
> >>>>>>>   lpbe
> >>>>>>>   bcfl sdh
> >>>>>>>   ion 1 0.000 2.0
> >>>>>>>   ion -1 0.000 2.0
> >>>>>>>   pdie 2.0
> >>>>>>>   sdie 78.00
> >>>>>>>   chgm spl0
> >>>>>>>   srfm smol
> >>>>>>>   srad 0.0
> >>>>>>>   swin 0.3
> >>>>>>>   sdens 10.0
> >>>>>>>   temp 298.15
> >>>>>>>   gamma 0.105
> >>>>>>>   calcenergy total
> >>>>>>>   calcforce no
> >>>>>>>   write pot dx complex
> >>>>>>> end
> >>>>>>>
> >>>>>>> quit
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> ------------------------------------------------------------------
> --
> >> --
> >>>>>>>
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> >>>>>>> _______________________________________________
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> >>>>>>> apb...@li...
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/apbs-users
> >>>>>>>
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Re: [Apbs-users] pka-balanol example and MMPBSA

Biomolecular electrostatics software

Re: [Apbs-users] pka-balanol example and MMPBSA