setbulk.inp memory problems

Magali Mathieu mathieu at lbs.cnrs-gif.fr
Wed Sep 2 12:46:50 EST 1998


I have memory problems when running setbulk.inp. The program insists in
calculating a map in P1 while in the mask subroutin, then crashes
because of space problems:

 XREFINE>   mask 
 MASK>     mode=vdw           { use vdw radii                     } 
 MASK>     solrad=1.0         { a probe radius adds to vdw radii  } 
 MASK>     shrink=1.1         { the shrink radius                 } 
 MASK>     nshell=1           { the number of shells              } 
 MASK>     to=mask            { output to the mask map            } 
 MASK>   end 
 XMASK:     3281 atoms have been selected for mask calculation.
 XMAPASU: using grid [256,256,256] and sublattice [128,128,128]
 %XASUDEF-warning: no asymmetric unit for maps specified.
 %XASUDEF-warning: excessive memory and CPU usage may occur.
 Maps will be stored in P1:
   A=     0,...,   255  B=     0,...,   255  C=     0,...,   255
 XMAPAL: allocating space for real space object.
 %VEHEAP-ERR: could not satisfy storage request for     9198947 bytes
 Subroutine DIE called . Terminating


How can I tell the mask subroutin to use the symmetry operators I
already gave xplor? How can I solve this storage problem?
My imput file follows.

	Thanks,
	Magali

 remarks  file xtalrefine/setup_bulksol.inp 
 
 topology
        reset
 end

 parameter
        reset
 end

  structure
         Reset
 end
 
 xrefin
	reset
 end

 structure 
	@pdb.psf		             { Read structure file            }
 end                 			     { Read structure file            }

 parameter 

   @/prog2/xtal/xplor3.84/toppar/parhcsdx.pro   { Read empirical
potential      }
  @parameter.elements                          
  nonbonded AD        0.1000   1.1500       0.1000 1.1500  
		{Cadmium values}
                                             { parameter
file                 }
                                           {*Append parameters for
waters.*}
   BOND HT   OT     450.0       0.9572    
   ANGLE HT   OT   HT      55.0     104.52    

                                           {*For solute-water
interactions.*}
   NONBONDED OT        0.1591   2.8509     0.1591   2.8509   
   NONBONDED HT        0.0498   1.4254     0.0498   1.4254   

                                            {*For water-water
interactions.*}
   !---------------A--------------B--------------A14-----------B14-----
   nbfix ot  ot  581980.4948  595.0436396     581980.4948  595.0436396
   nbfix ht  ht  3.085665E-06 7.533363E-04    3.085665E-06 7.533363E-04
   nbfix ht  ot  327.8404792  10.47230620     327.8404792  10.47230620 
   

   nbonds                                    { This statement specifies
the   }
      atom cdie shift eps=1.0  e14fac=0.4    { nonbonded interaction
energy   }
      cutnb=7.5 ctonnb=6.0 ctofnb=6.5        { options.  Note the
reduced     }
      nbxmod=5 vswitch                       { nonbonding cutoff to
save      }
   end                                       { some CPU
time                  }
 end
                                             { All charged groups
are         }
                                             { turned
off                     }
 vector do ( charge=0.0 ) ( resname LYS and 
    ( name ce or name nz or name hz* ) )     { Turn off charges on
LYS        }
 vector do ( charge=0.0 ) ( resname GLU and
    ( name cg or name cd or name oe* ) )     { Turn off charges on
GLU        }
 vector do ( charge=0.0 ) ( resname ASP and
    ( name cb or name cg or name od* ) )     { Turn off charges on
ASP        }
 vector do ( charge=0.0 ) ( resname ARG and
    ( name cd or name *E or name cz or name NH* or name HH* ) )
                                             { Turn off charges on
ARG        }

 flags                                       { In addition to the
empirical   }
    include pele pvdw xref                   { potential energy terms
which   }
    ?                                        { are turned on initially. 
This }
 end                                         { statement turns on
the         }
                                             { crystallographic residual
term }
                                             { and packing
term.              }

 			{atoms on the 3-fold axis}

 vector ident (store1) ((segid "Z   ") or (segid "Y   ") or (segid "C  
") )
  CONStraints
   INTERaction ( not ( store1 ) ) ( not ( store1) )
       weights * 1. end
   INTERACTIOn ( store1 ) ( store1 )
       weights * 1. pvdw 0. pele 0. end
  END
{ CONSTRAINTS
	FIX= (store1)
 END
}
xrefin
{===>}                                                { unit cell for
crystal }
     a=157.78  b=157.78   c=157.780  alpha=90.0 beta=90.0 gamma=90.00  
{ Unitcell }
{===>}
    symmetry=(x,y,z)   { operators for crystal symmetry P4132 }
    symmetry=(-x+1/2, -y,  z+1/2)  
    symmetry=(-x,  y+1/2, -z+1/2)  
    symmetry=( x+1/2, -y+1/2, -z)  
    symmetry=( z,  x,  y)  
    symmetry=( z+1/2, -x+1/2, -y) 
    symmetry=(-z+1/2, -x,  y+1/2) 
    symmetry=(-z,  x+1/2, -y+1/2)
    symmetry=( y,  z,  x)
    symmetry=(-y,  z+1/2, -x+1/2) 
    symmetry=( y+1/2, -z+1/2, -x) 
    symmetry=(-y+1/2, -z,  x+1/2) 
    symmetry=( y+3/4,  x+1/4, -z+1/4) 
    symmetry=(-y+3/4, -x+3/4, -z+3/4) 
    symmetry=( y+1/4, -x+1/4,  z+3/4) 
    symmetry=(-y+1/4,  x+3/4,  z+1/4) 
    symmetry=( x+3/4,  z+1/4, -y+1/4)
    symmetry=(-x+1/4,  z+3/4,  y+1/4) 
    symmetry=(-x+3/4, -z+3/4, -y+3/4) 
    symmetry=( x+1/4, -z+1/4,  y+3/4) 
    symmetry=( z+3/4,  y+1/4, -x+1/4) 
    symmetry=( z+1/4, -y+1/4,  x+3/4) 
    symmetry=(-z+1/4,  y+3/4,  x+1/4)
    symmetry=(-z+3/4, -y+3/4, -x+3/4)
                                     
            { The following contains the atomic form factors.  A
4-Gaussian   }
            { approximation is used.  Atoms are selected based on
their       }
            { chemical atom type.  Note the use of wildcards in the
selection } 

   SCATter ( chemical C* ) 
   2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512
.215600

   SCATter ( chemical N* )
   12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600
-11.529

   SCATter ( chemical O* )
   3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089
.250800

   SCATter ( chemical S* )
   6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720
.866900

   SCATter ( chemical P* )
   6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645
1.11490

   SCATter ( chemical FE* )
   11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566
0.97070

   SCATter ( chemical ZN* )
    14.0743 3.2655 7.0318 0.2333 5.1652 10.3163 2.41 58.7097 1.3041

  SCATter ( chemical AC* )
  8.6266 10.4421 7.3873 0.6599 1.5899 85.7484 1.0211 178.437 1.3751

  SCATter ( chemical AD*)
 15.6348 -0.00740 7.95180 0.608900 8.43720 10.3116 0.853700 25.9905
-14.875

  nreflections=50000  { This will allocate space for the list of
reflections } 
                       { specify a number greater or equal the acutal
number  }
                       { of
reflections                                       }



   reflection
     @file.cv
	               { Here we read in the diffraction data, }             
                       { A typical line in the file may look like
this:       }
                       { INDEx= -3 2 1 FOBS=5.956 WEIG= 1.0 PHASe=46.
FOM=0.4 }
                       { Everything is free-field, if you don't
specify       }
                       { something it'll be set to a reasonable default
value }
   end

   method=FFT          { Use the FFT method instead of direct
summation       }
   
   fft 
      grid = 0.33
      memory=5000000    { This tells the FFT routine how much physical
memory  }
   end                 { is available, the number refers to DOUBLE
COMPLEX    }
                       { words, the memory is allocated from the
HEAP         }
      

   ?                   { This prints the current
status                       }
	resolution  43 1.95
	print completeness
 end                  { This terminates the diffraction data
parser          }

 coordinates @pdb.xpdb         { Read coordinates               }
                                           { test set for
cross-validation. }
 
{===>}
 evaluate ($out_ref="sbulk.cv")    { Output reflection file.        }

{===>}
 evaluate ($low_res=43.0)                       {* low resolution
limit.  *}
 evaluate ($high_res=1.95)                        {* high resolution
limit. *}
 
{===>} 
 evaluate ($f_cut=0.0)                        {* F/sigma amplitude
cutoff. *}


{===>}                       {* Select atoms to be included in
refinement. *}
 vector ident (store1) (known) 

{===>}
 evaluate ($ncs_flag=NONE) { RESTRAIN or STRICT or NONE ! ncs
information.  }
 
{===>}
 evaluate ($k3=-9999.) {* Optional: fix set solvent density level by
setting}
                       {* this parameter to a positive
value.               }
                       
{===>}
 evaluate ($b3=-9999.) {* Optional: fix set solvent b-factor by
setting     }
                       {* this parameter to a positive
value.               }
           
!----------------------------------------------------------------------------

 xrefine

   resolution_limits= $low_res $high_res

   do (fobs=0) (amplitude(fobs) <= $f_cut * sigma) 

   method=FFT          
   
   fft 
      memory=5000000   
   end                 
   
 
   selection=( store1 ) 

end

 if ($ncs_flag=STRICT) then
    @@$ncs_file
 elseif ($ncs_flag=RESTRAIN) then
    @@$ncs_file
    flags include ncs end
 end if
              
xrefin
   
   update                        {*Update Fcalcs and print current
rfactor.*}
   
   print rfactor
   
end                  


 xrefine
   {* compute a solvent mask and store it in mask *}
   declare name=mask domain=real end
   mask               
     mode=vdw           { use vdw radii                     }
     solrad=1.0         { a probe radius adds to vdw radii  }
     shrink=1.1         { the shrink radius                 }
     nshell=1           { the number of shells              }
     to=mask            { output to the mask map            }
   end
   
   {* Fourier transformation of the solvent mask and store it in fpart*}
   do (fpart=ft(mask)) ( all )

   {* solvent parameters refinement via by the multiscale routine *}
   multiscale
      bfmin=0. bfmax=200.
      set1=fobs   k1=-1       b1=0
      set2=fcalc  k2=1.0      b2=0 
      set3=fpart  k3=$k3      b3=$b3        
      selection=( $high_res <= d <= $low_res 
             and test=0 )
      resk=5.0             { resolution boundary for two FFKs }
      update=false
      bmin=10.
      bmax=300.
      
      ?
   end

   {* compute refined solvent structure factors in fbulk *}
   do (fpart=$k3*exp(-$b3*s()*s()/4.0)*fpart) ( all )
   
   display  bulk solvent model parameters: density level = $k3 e/A^3, 
B-factor= $b3 A^2
   remarks  bulk solvent model parameters: density level = $k3 e/A^3, 
B-factor= $b3 A^2
   
   print rfactor
   
   do (fcalc=complex(0,0)) ( all )

                  {*Write a new reflection file including the solvent
FPART.*}
   write reflection 
      output=$out_ref sele=( all ) 
   end   

 end

 stop



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