CHARMM c42b2 gbmv.doc



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                 Generalized Born using Molecular Volume (GBMV)
                     Solvation Energy and Forces Module   
                                    - and -
                                  Surface Area 

     Questions and comments regarding GBMV should be directed to 

     Michael S. Lee or Michael Feig c/o 
     Charles L. Brooks, III (brooks@scripps.edu)

* Menu:

* Description:: Description of GBMV and related commands
* Syntax::      Syntax of the GBMV Commands
* Function::    Purpose of each of the commands
* Examples::    Usage examples of the GBMV module



File: GBMV -=- Node: Description
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Background:

    The GBMV module is a Generalized Born method for 
mimicking the Poisson-Boltzmann (PB) electrostatic solvation energy. The PB
method for obtaining solvation energies is considered a benchmark for implicit 
solvation calculations. However, the PB method is slow and the derivatives, 
i.e. forces, are ill-defined unless one changes the definition of the 
molecular volume.
     The Generalized Born equation, as prescribed by Still, et. al. allows
one to compute solvation energies very similar to the PB equations. 
As it is an analytical expression, forces are available as well:

                                                     q q
                              N   N                   i j
    G   =  -C  (1-1/eps){1/2 sum sum ------------------------------------ }
     pol     el              i=1 j=1 [r^2 + alpha *alpha exp(-D  )]^(0.5)
                                       ij        i      j      ij

           
    D   = r^2 / (K_s * alpha * alpha )
     ij    ij               i       j

where K_s = 4 for Still's original equation, or 8 for modified equation.
     The only problem is that one needs to calculate the alpha's, a.k.a.
Born radii for each atom, accurately. There are various methods available, 
such as the GBORN, ACE, and GBSW modules in CHARMM. 
     The GBMV method obtains the Born radii very accurately, 
i.e, w/ greater than 0.99 correlation. It is available as three approaches:

 1)  grid-based (Most accurate)
 2)  analytical method I (Least accurate, fastest)
 2)  analytical method II (preferred for dynamics)

The analytical method has derivatives and thus can be used in molecular 
dynamics simulations. The grid-based method has no derivatives, however, 
it is the most accurate and still can be used in energy ranking and 
Monte-Carlo methods.

When should you use GBMV?

     Because the analytical and grid-based methods are quite accurate, the
parameters change very little when optimized for a particular force-field. 
Hence, forcefields besides those of CHARMM can be used with GBMV without 
refitting of parameters. The GBMV method II approximates the molecular
surface directly. The agreement with respect to electrostatic solvation 
energies from standard Poisson theory is very good (<1% relative error). 
The higher accuracy comes at a price, however, and GBMV is slower than 
other GB methods in CHARMM.

Papers related to GBMV method: 

(1) M. S. Lee, F. R. Salsbury, Jr., and C. L. Brooks III. 
    J. Chem. Phys.(2002),116, 10606 
(2) M. S. Lee, M. Feig, F. R. Salsbury, Jr., and C. L. Brooks III. 
    J. Comp. Chem. (2003), 24, 1348 
(3) M. Feig, A. Onufriev, M. S. Lee, W. Im, D. A. Case, C. L. Brooks III,
    J. Comp. Chem. (2004), 25, 265-284
(4) S. Tanizaki, M. Feig, 
    J. Chem. Phys. (2005), 122, 124706
(5) J. Chocholousova, M. Feig,
    J. Comp. Chem. (2006) 27, 719-729 


Surface Area

     A solvent accessible surface area (SASA) calculation is implemented
within the GB module. There is essentially no additional cost compared to the 
GB calculation itself and about 5 times faster than an exact, analytical 
calculation (e.g. from the ASP module). It is accurate to within 1% of the 
exact surface and is much more accurate than the SASA module within CHARMM.
 


File: GBMV -=- Node: Syntax
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Syntax of Generalized Born Molecular Volume (GBMV) Solvation commands

[SYNTAX: GBMV commands]

[method I: faster but less accurate]

GBMV { P1 <real> P2 <real> LAMBda1 <real> DN <real> SHIFT <real> 
       WATR <real> BETA <real> EPSILON <real> 
       SA <real> SB <real> SCUT <real>} 
       [WEIGHT]
       [GBVDW]
       CORR <int> 
        { ESHIFT <real> SHIFT <real> TT <real>   (CORR = 0) }             
        { SHIFT <real> SLOPE <real>              (CORR = 1) }
     }

[method II: slower but more accurate (recommended)]

GBMV { [GEOM] [ARITH] [WEIGHT] [FIXA]
       BETA <real> EPSILON <real> DN <real> WATR <real> 
       LAMBDA1 <real> TOL <real> BUFR <real> MEM <int> CUTA <int> 
       HSX1 <real> HSX2 <real> ONX <real> OFFX <real> 
       ALFRQ <int> EMP <real> 
       P1 <real> P2 <real> P3 <real> P4 <real> P6 <real> 
       SA <real> SB <real> SCUT <real>
       KAPPA <real>
       WTYP <int> NPHI <int> 
       GBVDW
       CORR <int> 
        { ESHIFT <real> SHIFT <real> TT <real>   (CORR = 0,2) }             
        { SHIFT <real> SLOPE <real>              (CORR = 1,2) } 
        { A1 <real> A2 <real> A3 <real>          (CORR = 2) }
       GCUT <int>
       RADG <int> <real ...>
       FAST 1|0 SGBFRQ <int> SXD <real>
     }

[HDGB method: heterogeneous dielectric / membrane model]

GBMV { { GBMV II options }
      CORR <int> (CORR = 3, 4, 5)
      A1 <real> A3 <real> A4 <real> A5 <real>
      UNEPS <int> 
      ZS <real> ZM <real> ZT <real> ST0 <real>
      HDGBRC HDNOSW
     }

[ grid-based method ]

GBMV GRID { [GEOM] [ARITH] [CONV] [WEIGHT]
            EPSILON <int> DN <real> WATR <real> 
            P6 <real> 
            KAPPA <real>
            WTYP <int> NPHI <int> 
            CORR <int> 
            { SHIFT <real> SLOPE <real>     (CORR = 1) }
            { ESHIFT <real> SHIFT <real>    (CORR = 0) }         }
          }

[ free-up memory and/or start over]

GBMV CLEAr



File: GBMV -=- Node: Function
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          ---------------------------------------------------------------
          Parameters of the Generalized Born using Molecular Volume Model
          common to all methods:
          ---------------------------------------------------------------

WTYP      Angular integration grid type: 

            0 - Dodecahedron
            1 - Spherical polar 
            2 - Lebedev (DEFAULT)
            3 - Alternating octahedron/cube

NPHI      Used when WTYP equals 1 or 2. When WTYP=1, it corresponds to number
          of phi angles. When WTYP=2, it corresponds to size of 
          Lebedev grid, which can only have values of 6,26 (Default), and 38 
          at the present time.

CUTA      Extent of radial integration points in Angstroms. (Default 20)

GCUT      radial spacing of integration grid

            1 - default spacing:
                0.1 0.2  0.3 0.4 0.5 0.75 1.0 1.25
                1.5 1.75 2.0 2.5 3.0 3.5  4.0 5.0
                6.0 7.0  8.0 10.0 12.0 16.0 20.0

            2 - finer spacing for small radii
                0.1  0.2  0.3  0.4  0.5  0.6  0.8  1.0 
	        1.2  1.4  1.6  1.8  2.0  2.2  2.4  2.6
        	2.8  3.0  3.2  3.7  4.1  5.1  6.1  7.1
                8.1 10.1 12.1 16.1 20.1
           
            3 - custom grid, specify with RADG

RADG      custom grid spacing, first argument is number of intervals
          following arguments are interval limits

CORR      Coloumb field correction method: 

            0  for R^5 method.            use: SHIFT/ESHIFT/TT

               alpha(i) = - 1/( r4 - TT * r5 + ESHIFT ) + SHIFT

            1  for R^7 method (default)   use: SHIFT/SLOPE 
 
               alpha(i) = SLOPE/( (1-1/sqrt(2)) * r4 + r7) + SHIFT

            2  for R^5/R^7                use: A1/A2/A3/SHIFT/SLOPE/ESHIFT

	       alpha(i) = SLOPE/( A1 * r4 + A2 * r5 + A3 * r7 + ESHIFT) + SHIFT

               this mode is intended for the calculation of Born radii
               in different dielectric environments

            3  for R^5/R^7                use: A1/A3/A4/A5/SLOPE

	       alpha(i) = SLOPE/( A1 * r4 + A3(i) * r7) + A4 + A5/(eps(i) + 1)
               A3(i)    = A3 * 3 * eps(i) / (3 * eps(i) + 2 * EPS)

               this mode is intended for the implicit membrane model(see below)

            4  Same as CORR = 3 except that the local dielectric constant
               is modulated spherically.

            5  Same as CORR = 3 except that the local dielectric constant
               is modulated cylindrically.

          where r4 is volume integral over 1/r^4, r5 is square root
          of integral over 1/r^5 and r7 is integral over 1/r^7 to the 
          power of 1/4. 

TT        Multiplicative factor for correction term (CORR = 0 only). 

SHIFt     The shifting factor of Alpha(i).   MUST be set! 

ESHIft    Energy shifting factor of the self-polarization 
          energies: 1/Alpha(i). CORR=0 or 2 only. (Default 0.0)

SLOPE     Multiplicative factor of the Alpha(i). CORR=1 or 2 only. (Default 1)

A1,A2, A3 Multiplicative factors in calculation of Alpha(i). 

WATR      The radius of the water probe. Usually this is set to 1.4 
          Angstroms. If this were changed, other parameters would have 
          to be modified.

EPSILON   This is the value of the dielectric constant for the solvent medium.
          The default value is 80.

KAPPA     Debye-Huckel ionic term: Units of inverse length (Angs). Default
          is 0 (no salt).

GEOM      Select geometric cross-term in Still equation (default).

ARITH     Select arithmetic cross-term in Still equation.

P6        Exponent in exponential of Still equation. Default is 4, for
          historical reasons. Value of 8 is RECOMMENDED for GEOM, 6.5 for
          ARITH.
 
WEIGHT    Use WMAIN array for radii. (Default uses vdW radii array)

CLEAr     Clear all arrays and logical flags used in Generalized Born 
          calculation. Use command by itself.

          -----------------------------------------------------------
          Parameters specific to GBMV I and II:
          -----------------------------------------------------------

FIXA      Update alphas only if coordinates have changed more
          than expected for finite differences. Useful for
          static pka calculations. With FIXA keyword, finite-difference
          wouldn't work correctly, hence it must be specified. Not
          on by default. 

ALFRQ     Update frequency of Born radii. Use with great caution! 
          One of LIMP,IMP, or EMP options must be selected. (Default 1)
	  Values other 1 not generally recommended.

LIMP      Use ALFRQ*(dE/dalpha)(dalpha/dx) part of GB force every ALFRQ
          steps. For ALFRQ <= 5.

EMP       Decay constant of the impulse force. Default is 1.5, which
          is meant for ALFRQ of 5. Generally, EMP ~= ALFRQ/4. For 
          ALFRQ <= 10. (Recommended option)

IMP       Use (dE/dalpha)(dalpha/dx) part of GB force every ALFRQ
          steps. Any ALFRQ can be used. Only meant for equilibrium
          calculations.

DN        The cell width of the lookup grid. Larger values make program
          slower. Smaller values use up more memory. Default of 1.0 A is best
          compromise between speed and memory.

BETA      Smoothing factor for tailing off of volume. 
          Values of around -100 are fine for GBMV I. Values between -8 to 
          -50 are reasonable for GBMV II. (Default -20)

	  Smaller values of beta lead to more stable dynamics, but compromise
          the agreement with Poisson theory. In GBMV II the choice of BETA 
          also affects P3. Good pairs of values for GBMV II are:

             BETA = -20, P3 = 0.70
             BETA = -12, P3 = 0.65  * recommended as best compromise
             BETA = -10, P3 = 0.57
             BETA =  -8, P3 = 0.35

LAMBda    The threshold value for the atomic volumes. In GBMV I, smaller
          values produces shorter Born radii and wide variance w/respect
          to accurate PB radii. Large values produce larger radii but smaller 
          variance. In GBMV II, value should be kept at 0.5.

BUFR      Distance that any atom is allowed to move before lookup table
          is rebuilt. Larger values lead to less lookup table update but larger
          memory usage. Use 0.0 for static structure.
          Values between 0.2 and 1.0 Angstrom. (Default 0.5)

MEM       Percentage extra memory beyond hypothetical calculation of table
          size. (Default 10)

TOL       Accuracy of the switching function used to determine accuracy of the
          first derivatives, i.e. forces. (Default 1e-8)

SA        Surface area coefficient (KCAL/(MOL*A**2)). (Default 0.0)
          SASA Energy term shows up under EXTERN/ASP.

SB        Surface area constant (KCAL/MOL) (no effect on forces) (Default 0.0)

SON       The startpoint for the switching function of each hard sphere.
          (Default 1.2) Units in Angstroms

SOFF      The endpoint for the switching function of each hard sphere.
          (Default 1.5)

P1        The multiplicative factor for the exponent of the 
          quartic exponential atomic function:
                
                 Gamma(i) = P1 * log(lambda)/(Rad(i)^4)

          Parameters specific to GBMV II:

P1,P2     Variables which affect the shape of the VSA atomic function in the 
          region of R to R+2. 
 
                 F(x) = A^2 / (A + x^2 - R^2)^2

             where

                 A = P1 * R + P2 (Defaults: P1 = 1.25/P2 = 0.45)

P3        Scaling factor of VSA function. Default = 0.7 
          This factor depends on the value chosen for BETA 
          (see description above)

P4        Scaling coefficient for correction term to Still's equation.
          (set to 0.0 for now)

P5        Exponent to the Still correction term. (use default for now)

HSX1/HSX2 Start and stop of hard-sphere tail with R(vdW) as origin.
          (Defaults: -0.125/0.25).

ONX/OFFX  Start and stop of VSA tail. Increasing values up to 2.8 A 
          makes better accuracy, however slows calculation. Compromise
          of 1.9/2.1 is default.

FAST      Turns on fast GBMV routine.

SGBFRQ    Update frequency of internal lookup list in fast GBMV mode 
          (Default 1). Values between 1 and 10 are recommended.

SXD       Delta used in fast GBMV mode lookup buffer. (Default 0). 
          Recommended values between 0.1 and 0.5. Requires 'FAST 1'

GBVDW     If present, the VDW dispersion term is turned on.

GBASP     If present, variable surface area coefficients are turned on.
          They are read from the ASPValue array that should be set
          before calling GBMV with appropriate scalar commands.

          -----------------------------------------------------------
          Parameters specific to HDGB (CORR = 3, 4, 5):
          -----------------------------------------------------------

UNEPS     Unit number of an input file holding the dielectric profile
          values (Use -1 for the default profile).  The format of this
          input file is restricted.  Comments are not allowed in a file.
          The dielectric profile must be sampled in equal intervals.
          The first line needs the number of sampling points n and the
          sampling interval h (Angstrom). Two columns of the z coordinates
          (Angstrom) and dielectric constants. The example is given 
          in test/data/hdgb_eps.dat.
  
A4,A5     Parameters in calculation of Alpha(i). A4 and A5 correspond
          to the parameter D and E of Equation (15) in the reference (3)
          respectively. 


ZS,ZM,ZT  Parameters for a switching function for the nonpolar energy.
ST0       ZS, ZM, ZT, and ST0 corresponds to Za, Zb, Zc, and C of
          Equation (11) in the reference (4).

UNNP      Unit number of a previously opened (formatted) input file for 
          the non-polar profile. If this option is used the values given 
          with ZS, ZM, ZT, and ST0 are ignored. The format is the same
          as the format used for the dielectric profile (see UNEPS).

HDGBRC    If this flag is specified, the radius will be corrected
          upon insertion to an implicit membrane.
          (Only availabe for CORR = 3)

HDNOSW    Turn off switching function for non-polar part when in HDGB 
          mode (CORR = 3,4,5)

          -----------------------------------------------------------
          Parameters specific to HDGBVDW (VDW dispersion term) (CORR = 3):
          -----------------------------------------------------------

GBVD      If present, the VDW dispersion term is turned on.

UNDO      Unit number (81) of a previously opened density profile file for water
          molecules. The format used for UNDO and other density profile files
          (see below: UNDP, UNDC, UNDC2 and UNDN) is the same as the format
          used for dielectric and non-polar profiles (see UNESP).           

UNDP      Unit number (82) of a previously opened density profile for oxygen 
          atoms of lipid molecules.

UNDC      Unit number (83) of a previously opened density profiles for carbon 
          atoms at the head group of the lipid molecules.

UNDC2     Unit number (84) of a previously opened density profiles for carbon
          atoms at the tail of the lipid molecules.

UNDN      Unit number (85) of a previously opened density profiles for hydrogen 
          atoms of lipid molecules.

          -----------------------------------------------------------
          Parameters specific to DHDGB (CORR=3)
          -----------------------------------------------------------
          PLEASE NOTE THAT DHDGB HAS ONLY BEEN TESTED WITH DEFAULT PREF.DAT
          WE STRONGLY ADVISE AGAINST USING THIS KEY WORD ALONG NON-DEFUALT
          ONES.
          This is an extension of HDGB implicit membrane
          with CORR=3 (planer membrane).
          DHDGB will allow planer membranes local thickness to vary
          dynamically. For more information about the DHDGB model please
          refer to Panahi A., Feig M., JCTC 2013, 9, 1709-1719.
          Attention:
          Please note that this model is only developed to be used with
          single-pass transmembrane helices with radius of 7.5 A
          For now, DHDGB only works for energy calculations (using energy
          command), minimizations using SD and ABNR methods and VVER
          integrator with Nose-Hoover thermostate (NVT ensemble)

QDHDGB    keyword for turning membrane local fluctuation on
UNFHDGB   unit number of a binary coefficient file that includes the
          coefficients of spline interpolation of deformation energy.
          Please use test/data/small_lookup_coeffs.bin as an example 
          for this unit. This file must meet specific criteria: 
          1. it has to be a binary file with size of real 4
          2. it contains spline coefficients for deformation energy values
              that exhustively sample between 35 to 0 A (membrane thickness)
              with 5 A intervals
          3. Since there are 7 intervals and each have one cubic term 
             (with 4 coefficients) the dimension of the number of coefficients
             will be (4*7)^(ANGDIM) where ANGDIM can be either 3 or 5.  

UNEPS_DEF_A,
UNEPS_DEF_C,    adjustable a{epsilon}, c{epsilon} and e{epsilon}
UNEPS_DEF_E     of equation 24 above reference. The format of these files
                are the same as UNEPS and UNNP in HDGB. To see an example
                please see test/data/coeff_a_eps.txt,
                test/data/coeff_c_eps.txt,test/data/coeff_e_eps.txt

UNNP_DEF_A,
UNNP_DEF_C,     adjustable a{gamma}, c{gamma} and e{gamma}
UNNP_DEF_E      of equation 27 above reference,The format of these files
                are the same as UNEPS and UNNP in HDGB. To see an example
                please see test/data/coeff_a_np.txt,
                test/data/coeff_c_np.txt,test/data/coeff_e_np.txt


CIRCLERAD       7.5 radius of the inclusion cylinder
SMASS           mass of virtual particles that represent the local position
                membrane around the inclusion

ANGDIM          3 or 5 the number of S values on the contact circle. 
                The smallest value allowed is 3 and the biggest value is 5.
                Please note that the file that contains the 
                cubic SPLINE coefficients must match the dimensions of 
                the s values (4*27)^(ANGDIM). We recommend using 5 S values for
                each leaflet. 

SDEF(1),...     25 initial position of the virtual particles
SDEF(10)

Please Note that during minimization the values of SDEF will be written in
units 120 for SD and 121 for ABNR respectively.
For now DHDGB is NOT compatible with GBMVFA option.


          -----------------------------------------------------------
          Parameters specific to Grid-based GBMV:
          -----------------------------------------------------------

ML        Number of surface points to carve out re-entrant surface

CONV      Smear grid with cross-shaped blur function to improve accuracy

          -----------------------------------------------------------
          Additional parameters added for use with CPHMD:
          -----------------------------------------------------------
HYBRID    Keyword to invoke hybrid-solvent CPHMD. Allows GB radii
          to be calculated be considering only a subset of the entire
          system. ie. Ignoring solvent atoms
          Used in conjuction with atom-selection

SELE      Use the SELE keyword to manually specify atoms which will be
          considered in the calculation of Born radii for use with CPHMD  
          *** note : GBMV does not currently support images,
              therefore care should be used when attempting
              to use GBMV with hybrid solvent PHMD using
              periodic boundary conditions    



File: GBMV -=- Node: Examples
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                  Usage Examples and Compatibility


The examples below illustrate some of the uses of the generalized Born
Molecular Volume (GBMV) module.  See c29test/gbmvtest.inp for more examples.

--------------------------------------
THERE ARE TWO REQUIREMENTS TO RUN GBMV
--------------------------------------
1) Coordinates MUST be defined for all atoms before invoking the GBMV keyword.
   Otherwise, "infinite" grid is established which uses too much memory.

2) CUTOFF Parameters MUST be defined. 
   For non-infinite cutoffs, "switch" in nonbonded parameters is NECESSARY.

Example 1

  !To perform a single-point energy calculation w/infinite cutoffs using
  !GBMV I algorithm (any forcefield):

  scalar wmain = radii 

  GBMV BETA -100 EPSILON 80 DN 1.0 WATR 1.4 TT 2.92 -
       SHIFT -0.5 ESHIFT 0.0 LAMBDA1 0.1 P1 0.44 -
       BUFR 0.5 Mem 20 CUTA 20 WTYP 0 -
       WEIGHT ! Radii from wmain

  ENERGY ctonnb 979 ctofnb 989 cutnb 999

Example 2

  !To perform a single-point energy calculation w/infinite cutoffs using
  !the GBMV II algorithm (any forcefield):

  GBMV BETA -20 EPSILON 80 DN 1.0 watr 1.4 GEOM -
       TOL 1e-8 BUFR 0.5 Mem 10 CUTA 20 HSX1 -0.125 HSX2 0.25 -
       ALFRQ 1 EMP 1.5 P4 0.0 P6 8.0 P3 0.70 ONX 1.9 OFFX 2.1 -
       WTYP 2 NPHI 38 SHIFT -0.102 SLOPE 0.9085 CORR 1

  ENERGY ctonnb 979 ctofnb 989 cutnb 999
 
  GBMV CLEAR ! Clear GB arrays

Example 3

  !Recommended setup for molecular dynamics simulations with
  !the GBMV II algorithm:

  UPDATE atom CDIE eps 1 cutnb 21 ctofnb 18 ctonnb 16 switch vswitch

  GBMV EPSILON 80 BUFR 0.2 MEM 20 CUTA 20 ALFRQ 1 -
       GEOM BETA -12 P1 0.45 P2 1.25 P3 0.65 P6 8.0 - 
       CORR 1 SHIFT -0.1 SLOPE 0.9 WTYP 1 NPHI 5 -
       FAST 1 SGBFRQ 4 SXD 0.3

  !You should use Langevin dynamics and a 1.5 fs time step (with SHAKE)
  !is recommended for optimal stability. Many applications will also
  !tolerate 2 fs time step 
  !(more info in: Chocholousova & Feig, JCC (2006) 27, 719-729) 

  SHAKE BONH TOL 1E-08 PARAM

  SCALAR FBETA SET 10 SELECT .not. TYPE H* END

  DYNAMICS LEAP LANG START TIMESTEP 0.0015 NSTEP 1000 -
        FIRSTT 298 FINALT 298 BYCB -
        INBFREQ -1 IASORS 1 IASVEL 1 NPRINT 100 IPRFRQ 100 NSAVC 100 -
	ECHECK 20 TBATH 298 RBUF 0 ILBFREQ 50 -
        IUNVEL -1 IUNREA 11 IUNWRI 12 IUNCRD 13 KUNIT -1

Example 5 

  !Grid-based GBMV:

  GBMV GRID EPSILON 80 DN 0.2 watr 1.4 GEOM P6 8.0 -
       WTYP 0 NPHI 10 SHIFT -0.007998 SLOPE 0.9026 CORR 1 CONV

  ENERGY ctonnb 979 ctofnb 989 cutnb 999

Example 6

  ! HDGB DPPC membrane
  ! If you want the default DPPC profile used in the reference (4),
  ! comment out the open file statement and set UNEPS to -1.

  ! The input file will be closed automatically, so you don't need
  ! the explicit close statement.
  open unit 1 name eps.dat read form

  GBMV A1 0.3255 A3 1.085 A4 -0.14 A5 -0.15 -
       UNEPS 1 -
       ZS 0.5 ZM 9.2 ZT 25 ST0 0.32 
  
  ENERGY ctonnb 979 ctofnb 989 cutnb 999

Example 7

  ! HDGBVDW DPPC membrane

  open unit 89 name hdgbvdw_eps.dat read form
  open unit 88 name hdgbvdw_np.dat read form

  open unit 81 name hdgbvdw_water.txt read form
  open unit 82 name hdgbvdw_o.txt read form
  open unit 83 name hdgbvdw_c.txt read form
  open unit 84 name hdgbvdw_cc.txt read form
  open unit 85 name hdgbvdw_h.txt read form

  GBMV GBVD -
       CORR 3 -
       UNEPS 89 UNNP 88 -
       UNDO 81 UNDP 82 UNDC 83 UND2C 84 UNDN 85 -
       SA 0.038 SB 0

  ENERGY ctonnb 979 ctofnb 989 cutnb 999

----------------------------------------------------------------------
  <Known Compatible with>
   - PARALLEL
   - CONS FIX
   - INTE
   - PHMD
   - VIBRAN (finite difference second derivatives)
   - MMFF (WEIGHT keyword must be used)
   
  <Known Incompatible with (so far)> 
   - VIBRAN (no analytic second derivatives)
   - BLOCK (hence not compat. w/ PERT/PIMPLEM/PERTURB/REPLICA)
   - IMAGE/CRYSTAL
   - EWALD 
   - multiple dielectric
   - QUANTUM* (single energy with original charges is ok)
   - FLUCQ
   - GAMESS
   - GENBORN
   - GRID
   - PRESSURE
   - SBOUND

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