Mon Oct 10 14:04:02 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:04:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5517 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5060555 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 8.033999 61.68000 ymin,ymax (A): 56.18900 126.5370 zmin,zma (A): 28.98200 96.61400 x,y,z range (A): 53.64600 70.34801 67.63200 scale (grids/A): 0.5060555 object centre (A): 34.85700 91.36300 62.79800 number of atom coordinates read : 5517 total number of charged atoms : 5347 net assigned charge : 4.034031 assigned positive charge : 861.0984 centred at (gu) : 89.57420 89.56398 90.63264 assigned negative charge : -857.0720 centred at (gu) : 89.59055 89.53782 90.50929 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8427 nv = 96 ne = 84 npr = 112752 no. pairs analyzed = 112752 no. exposed pairs = 6614 no. arc points = 45456 no. surface atoms = 2223 nbur = 3294 mkacc time = 0.2700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 297 mr = 4438 m= 0 mr = 5 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5900000 number of dielectric boundary points 4281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4336 ## 668 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 11626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3279832E-10 4.2116025E-10 midg,1,midg; midg,igrid,midg -2.5608226E-11 9.9284019E-11 1,midg,midg; igrid,midg,midg 9.6732740E-11 2.6518015E-12 gauss-seidel spectral radius is 0.9800683 estimated iterations to convergence 59 setup time was (sec) 0.8300000 now iterating at: 14:04:03 rms-change max change #iterations 7.0897602E-02 11.05014 at 10iterations 4.9065747E-03 0.6628456 at 20iterations 8.5760513E-04 0.1033993 at 30iterations 2.7453486E-04 3.7933350E-02 at 40iterations 9.3074763E-05 1.3846397E-02 at 50iterations finished qdiffx linear iterations at : 14:04:06 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 9.3074763E-05 1.3846397E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:04:06 3.656u 0.155s 0:04.53 83.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:04:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5517 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.518167 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 8.033999 61.68000 ymin,ymax (A): 56.18900 126.5370 zmin,zma (A): 28.98200 96.61400 x,y,z range (A): 53.64600 70.34801 67.63200 scale (grids/A): 1.518167 object centre (A): 34.85700 91.36300 62.79800 number of atom coordinates read : 5517 total number of charged atoms : 5347 net assigned charge : 4.034031 assigned positive charge : 861.0984 centred at (gu) : 88.72092 88.69015 91.89595 assigned negative charge : -857.0720 centred at (gu) : 88.77168 88.61302 91.52798 start vw surface at 0.2400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 96569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45456 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27033 mr = 66935 m= 2235 mr = 18014 m= 52 mr = 925 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1800 time to turn everything in is 0.7200000 number of dielectric boundary points 40012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 666 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 39921 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5060555 object centre at (A) : 34.85700 91.36300 62.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5916094E-02 1.2992884E-02 midg,1,midg; midg,igrid,midg -9.7765196E-03 3.6896896E-04 1,midg,midg; igrid,midg,midg 4.5342343E-03 3.3867247E-03 gauss-seidel spectral radius is 0.9981194 estimated iterations to convergence 183 setup time was (sec) 1.000000 now iterating at: 14:04:08 rms-change max change #iterations 4.137152 150.8397 at 10iterations 1.693659 60.01230 at 20iterations 0.6948276 22.56439 at 30iterations 0.2873460 8.637213 at 40iterations 0.1177024 4.183411 at 50iterations 4.8679981E-02 1.397617 at 60iterations 2.0153396E-02 0.5945454 at 70iterations 8.3979229E-03 0.2459027 at 80iterations 3.5811111E-03 0.1022758 at 90iterations 1.6170237E-03 5.0262451E-02 at 100iterations 7.8807719E-04 2.6287794E-02 at 110iterations 4.3382379E-04 1.3481140E-02 at 120iterations finished qdiffx linear iterations at : 14:04:14 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 4.3382379E-04 1.3481140E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 14:04:15 7.681u 0.184s 0:08.26 95.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:04:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5517 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.277250 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 8.033999 61.68000 ymin,ymax (A): 56.18900 126.5370 zmin,zma (A): 28.98200 96.61400 x,y,z range (A): 53.64600 70.34801 67.63200 scale (grids/A): 2.277250 object centre (A): 34.85700 91.36300 62.79800 number of atom coordinates read : 5517 total number of charged atoms : 5347 net assigned charge : 4.034031 assigned positive charge : 861.0984 centred at (gu) : 88.08076 88.03467 92.84333 assigned negative charge : -857.0720 centred at (gu) : 88.15746 87.91975 92.29184 start vw surface at 0.2300000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 225859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45456 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98093 mr = 165230 m= 23893 mr = 76412 m= 3119 mr = 17204 m= 167 mr = 1814 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 5857 time to turn everything in is 1.680000 number of dielectric boundary points 90414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 42639 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.518167 object centre at (A) : 34.85700 91.36300 62.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2358505 6.8826415E-02 midg,1,midg; midg,igrid,midg -7.4056067E-02 -6.5340400E-03 1,midg,midg; igrid,midg,midg 8.6107731E-02 6.9131121E-02 gauss-seidel spectral radius is 0.9991718 estimated iterations to convergence 274 setup time was (sec) 1.990000 now iterating at: 14:04:17 rms-change max change #iterations 11.21675 273.1676 at 10iterations 6.384778 145.7786 at 20iterations 3.629689 92.84763 at 30iterations 2.051716 41.33282 at 40iterations 1.156810 23.97146 at 50iterations 0.6507411 12.17209 at 60iterations 0.3656369 8.225592 at 70iterations 0.2051177 3.987812 at 80iterations 0.1147891 2.136272 at 90iterations 6.4155810E-02 1.218870 at 100iterations 3.5841897E-02 0.6371994 at 110iterations 2.0000828E-02 0.3454046 at 120iterations 1.1183796E-02 0.2146072 at 130iterations 6.2479740E-03 0.1180344 at 140iterations 3.4975207E-03 6.4690590E-02 at 150iterations 1.9624103E-03 3.8293839E-02 at 160iterations 1.1094727E-03 1.9999504E-02 at 170iterations 6.3382270E-04 1.1680126E-02 at 180iterations finished qdiffx linear iterations at : 14:04:27 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 6.3382270E-04 1.1680126E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 14:04:28 12.629u 0.197s 0:13.33 96.0% 0+0k 0+0io 0pf+0w