Hi Ray,
The atom "C4" which is of CG atom type is from receptor.
My RECEPTOR = branched polymer (PPI dendrimer) decorated on surface with
maltose or maltotriose units
I used combination of GAFF and Glycam ff here.
My LIGAND = small molecule ANS ( 8-Anilinonaphthalene-1-sulfonate )
parametrised using GAFF forcefield.
After reading this information from Amber11 manual:
------------------------------------------------------------------------------------------------------------
The new method separates nonpolar contribution into two terms: the
attractive (dispersion) and repulsive
(cavity) interactions. Doing so significantly improves the correlation
between the cavity free
energies and solvent accessible surface areas for branched and cyclic
organic molecules.[236]
-------------------------------------------------------------------------------------------------------------
I was thinking that for my system might be a new approach:
Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SASA + SURFOFF
better that the original one ( Gnp = SURFTEN * SASA + SURFOFF ).
There is no problem with GAFF atom types as radii are probably
automatically read from PRMTOP file.
The problem is just with Glycam CG atom type. I proved it by changing CG
to CT in prmtop file.
Anyway if I understood well the new approach for calculation of nonpolar
solvent contribution is actually
applicable (with sufficient reliability) probably just for standard atom
types from proteins, nucleic acids force-fields
( ff99SB, ff99bsc0 etc. ) because only for such atomtypes are in this
moment available optimised (Tan & Luo) radii which
might be probably considerably different from those in PRMTOP file. Am I
right ?
Best wishes,
Marek
Dne Wed, 16 Mar 2011 05:43:46 +0100 Ray Luo, Ph.D. <ray.luo.uci.edu>
napsal/-a:
> Dear Marek,
>
> It looks like the atom is part of a ligand, with its prmtop file
> generated
> by antechamber, I guess. Unfortunately, the nonpolar solvent model for
> general organic molecules has yet been trained ... Neither radiopt=1 nor
> radiopt=0 would work for ligand molecules ...
>
> All the best,
> Ray
>
> On Tue, Mar 15, 2011 at 6:45 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> Dear all,
>>
>> recently I wanted to do MM/PBSA analysis of my system using mm_pbsa.pl
>> script (AmberTools 1.4)
>> using INP=2 as it is recommended for case of branched and cyclic
>> molecules
>> in Amber manual.
>> As recommended for this choice I also set RADIOPT=1.
>>
>> Unfortunately calculation crashed with this error:
>>
>>
>>
>> PB Bomb in pb_aaradi(): No radius assigned for atom 616 C4 CG
>>
>>
>> when I tried to use RADIOPT=0 to force reading atom radii from PRMTOP
>> file, it crashed immediately
>> with no error message written in any output file.
>>
>> It seems that RADIOPT=1 is really mandatory for INP=2.
>>
>>
>> My interpretation of the above error is that Tan & Luo radius for Glycam
>> atom type "CG" is
>> unknown. If I am right I just don.t understand why in such case atom
>> radius from PRMTOP file
>> is not automatically used like in case of GAFF ( lowercase ) forcefield.
>>
>>
>> I would be grateful for any useful advice here (To change all CG to CT
>> in
>> prmtop file (just for PB calculation) ? or to add some lines in relevant
>> Amber source file ? ...).
>>
>> Thanks in advance !
>>
>> Best wishes,
>>
>> Marek
>>
>>
>>
>> Here is for completnes relevant part of my MM/PBSA input file:
>>
>> #
>> # Input parameters for mm_pbsa.pl
>> #
>> # Holger Gohlke
>> # 25.02.2010
>> #
>>
>> ################################################################################
>> .GENERAL
>> #
>> # General parameters
>> # 0: means NO; >0: means YES
>> #
>> # mm_pbsa allows to calculate (absolute) free energies for one
>> molecular
>> # species or a free energy difference according to:
>> #
>> # Receptor + Ligand = Complex,
>> # DeltaG = G(Complex) - G(Receptor) - G(Ligand).
>> #
>> # VERBOSE - If set to 1, input and output files are not removed. This
>> is
>> useful for
>> # debugging purposes.
>> # PARALLEL - If set to values > 1, energy calculations for snapshots
>> are
>> done
>> # in parallel, using PARALLEL number of threads.
>> #
>> # PREFIX - To the prefix, "{_com, _rec, _lig}.crd.Number" is added
>> during
>> # generation of snapshots as well as during mm_pbsa
>> calculations.
>> # PATH - Specifies the location where to store or get snapshots.
>> # START - Specifies the first snapshot to be used in energy
>> calculations
>> (optional, defaults to 1).
>> # STOP - Specifies the last snapshot to be used in energy calculations
>> (optional, defaults to 10e10).
>> # OFFSET - Specifies the offset between snapshots in energy
>> calculations
>> (optional, defaults to 1).
>> #
>> # COMPLEX - Set to 1 if free energy difference is calculated.
>> # RECEPTOR - Set to 1 if either (absolute) free energy or free energy
>> # difference are calculated.
>> # LIGAND - Set to 1 if free energy difference is calculated.
>> #
>> # COMPT - parmtop file for the complex (not necessary for option GC).
>> # RECPT - parmtop file for the receptor (not necessary for option GC).
>> # LIGPT - parmtop file for the ligand (not necessary for option GC).
>> #
>> # GC - Snapshots are generated from trajectories (see below).
>> # AS - Residues are mutated during generation of snapshots from
>> trajectories.
>> # DC - Decompose the free energies into individual contributions
>> # (only works with MM and GB).
>> #
>> # MM - Calculation of gas phase energies using sander.
>> # GB - Calculation of desolvation free energies using the GB models in
>> sander
>> # (see below).
>> # PB - Calculation of desolvation free energies using delphi (see
>> below).
>> # Calculation of nonpolar solvation free energies according to
>> # the INP option in pbsa (see below).
>> # MS - Calculation of nonpolar contributions to desolvation using
>> molsurf
>> # (see below).
>> # If MS == 0 and GB == 1, nonpolar contributions are calculated
>> with the
>> # LCPO method in sander.
>> # If MS == 0 and PB == 1, nonpolar contributions are calculated
>> according
>> # the INP option in pbsa (see below).
>> # NM - Calculation of entropies with nmode.
>> #
>> VERBOSE 0
>> PARALLEL 2
>> #
>> PREFIX snap
>> PATH ../0_snaps
>> START 399
>> STOP 400
>> OFFSET 1
>> #
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> #
>> COMPT ../prmtop/com.prmtop
>> RECPT ../prmtop/rec.prmtop
>> LIGPT ../prmtop/lig.prmtop
>> #
>> GC 0
>> AS 0
>> DC 0
>> #
>> MM 1
>> GB 0
>> PB 1
>> MS 0
>> #
>> NM 0
>> #
>>
>> ################################################################################
>> .PB
>> #
>> # PB parameters (this section is only relevant if PB = 1 above)
>> #
>> # The following parameters are passed to the PB solver.
>> # Additional input parameters may also be added here. See the sander
>> PB
>> # documentation for more options.
>> #
>> # PROC - Determines which method is used for solving the PB equation:
>> # By default, PROC = 2, the pbsa program of the AMBER suite is
>> used.
>> # REFE - Determines which reference state is taken for PB calc:
>> # By default, REFE = 0, reaction field energy is calculated
>> with
>> # EXDI/INDI. Here, INDI must agree with DIELC from MM part.
>> # INDI - Dielectric constant for the solute.
>> # EXDI - Dielectric constant for the surrounding solvent.
>> # ISTRNG - Ionic strength (in mM) for the Poisson-Boltzmann solvent.
>> # PRBRAD - Solvent probe radius in Angstrom:
>> # 1.4: with the radii in the prmtop files. Default.
>> # 1.6: with the radii optimized by Tan and Luo (In
>> preparation).
>> # See RADIOPT on how to choose a cavity radii set.
>> # RADIOPT - Option to set up radii for PB calc:
>> # 0: uses the radii from the prmtop file. Default.
>> # 1: uses the radii optimized by Tan and Luo (In preparation)
>> # with respect to the reaction field energies computed
>> # in the TIP3P explicit solvents. Note that optimized radii
>> # are based on AMBER atom types (upper case) and charges.
>> # Radii from the prmtop files are used if the atom types
>> # are defined by antechamber (lower case).
>> # SCALE - Lattice spacing in no. of grids per Angstrom.
>> # LINIT - No. of iterations with linear PB equation.
>> # IVCAP - If set to 1, a solvent sphere (specified by
>> CUTCAP,XCAP,YCAP,
>> # and ZCAP) is excised from a box of water. If set to 5, a
>> solvent shell
>> # is excised, specified by CUTCAP (the thickness of the shell
>> in
>> A).
>> # The electrostatic part
>> # of the solvation free energy is estimated from a linear
>> response
>> # approximation using the explicit water plus a reaction field
>> # contribution from outside the sphere (i.e., a hybrid
>> solvation
>> approach
>> # is pursued). In addition, the nonpolar
>> # contribution is estimated from a sum of (attractive)
>> dispersion
>> # interactions calc. between the solute and the solvent
>> molecules
>> # plus a (repulsive) cavity contribution. For the latter,
>> # the surface calculation must be done with MS = 1 and the
>> PROBE
>> should
>> # be set to 1.4 to get the solvent excluded surface.
>> # CUTCAP - Radius of the water sphere or thickness of the water shell.
>> # Note that the sphere must enclose the whole solute.
>> # XCAP - Location of the center of the water sphere.
>> # YCAP
>> # ZCAP
>> #
>> # NP Parameters for nonpolar solvation energies if MS = 0
>> #
>> # INP - Option for modeling nonpolar solvation free energy.
>> # See sander PB documentation for more information on the
>> # implementations by Tan and Luo (In preparation).
>> # 1: uses the solvent-accessible-surface area to correlate
>> total
>> # nonpolar solvation free energy:
>> # Gnp = SURFTEN * SASA + SURFOFF. Default.
>> # 2: uses the solvent-accessible-surface area to correlate the
>> # repulsive (cavity) term only, and uses a surface-integration
>> # approach to compute the attractive (dispersion) term:
>> # Gnp = Gdisp + Gcavity
>> # = Gdisp + SURFTEN * SASA + SURFOFF.
>> # When this option is used, RADIOPT has to be set to 1,
>> # i.e. the radii set optimized by Tan and Luo to mimic Gnp
>> # in TIP3P explicit solvents. Otherwise, there is no guarantee
>> # that Gnp matches that in explicit solvents.
>> # SURFTEN/SURFOFF - Values used to compute the nonpolar
>> # solvation free energy Gnp acccording to INP.
>> # If INP = 1 and RADIOPT = 0 (default, see above),
>> # use SURFTEN/SURFOFF parameters that fit with the radii from
>> the
>> # prmtop file, e.g., use SURFTEN: 0.00542; SURFOFF: 0.92 for
>> PARSE radii.
>> # If INP = 2 and RADIOPT = 1, these two lines
>> # can be removed, i.e. use the default values set in pbsa
>> # for this nonpolar solvation model. Otherwise, please
>> # set these to the following: SURFTEN: 0.04356; OFFSET: -1.008
>> #
>> # NP Parameters for nonpolar solvation energies if MS = 1
>> #
>> # SURFTEN/SURFOFF - Values used to compute the nonpolar contribution
>> Gnp
>> to
>> # the desolvation according to either
>> # (I) Gnp = SURFTEN * SASA + SURFOFF (if IVCAP = 0) or
>> # (II) Gnp = Gdisp + Gcavity = Gdisp + SURFTEN * SESA +
>> SURFOFF
>> (if IVCAP > 0).
>> # In the case of (I), use parameters that fit with the radii
>> from the
>> # reaction field calculation. E.g., use SURFTEN: 0.00542,
>> SURFOFF: 0.92
>> # for PARSE radii or use SURFTEN: 0.005, SURFOFF: 0.86 for
>> Tan &
>> Luo radii.
>> # In the case of (II), use SURFTEN: 0.069; SURFOFF: 0.00 for
>> calculating the
>> # Gcavity contribution.
>> #
>> PROC 2
>> REFE 0
>> INDI 1.0
>> EXDI 80.0
>> SCALE 3
>> LINIT 1000
>> PRBRAD 1.4
>> ISTRNG 0.0
>> RADIOPT 1
>> INP 2
>> #
>> #SURFTEN 0.00542
>> #SURFOFF 0.92
>> #
>> IVCAP 0
>> CUTCAP -1.0
>> XCAP 0.0
>> YCAP 0.0
>> ZCAP 0.0
>> #
>>
>> ################################################################################
>>
>>
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>>
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Received on Thu Mar 17 2011 - 04:00:02 PDT
