Sun Oct 9 15:00:33 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 Sun Oct 9 2011 at 15:00:33 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7997125 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): -42.23100 -6.504000 ymin,ymax (A): 4.829000 38.35600 zmin,zma (A): 17.16400 61.68000 x,y,z range (A): 35.72700 33.52700 44.51600 scale (grids/A): 0.7997125 object centre (A): -24.36750 21.59250 39.42200 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.514006 assigned positive charge : 164.8092 centred at (gu) : 90.19694 89.65652 88.92085 assigned negative charge : -163.2951 centred at (gu) : 90.25801 89.44714 89.08317 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5159 nv = 96 ne = 84 npr = 23655 no. pairs analyzed = 23655 no. exposed pairs = 1470 no. arc points = 10352 no. surface atoms = 489 nbur = 649 mkacc time = 5.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 2860 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.1900000 number of dielectric boundary points 2614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 675 ## 54 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 4676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1587222E-07 -1.4410753E-07 midg,1,midg; midg,igrid,midg -2.7027423E-07 3.9172710E-07 1,midg,midg; igrid,midg,midg 1.7847613E-07 -1.1264546E-08 gauss-seidel spectral radius is 0.9917414 estimated iterations to convergence 89 setup time was (sec) 0.4000000 now iterating at: 15:00:34 rms-change max change #iterations 0.2371079 35.13184 at 10iterations 3.5994880E-02 7.084324 at 20iterations 5.6470404E-03 0.8214476 at 30iterations 8.6633593E-04 0.1306229 at 40iterations 1.3265936E-04 1.9155979E-02 at 50iterations finished qdiffx linear iterations at : 15:00:36 total time elapsed so far: 2.830000 # loops : 50 mean,max change (kT/e) : 1.3265936E-04 1.9155979E-02 energy calculations done at 2.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 15:00:37 2.996u 0.162s 0:03.48 90.5% 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 Sun Oct 9 2011 at 15:00:37 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.399137 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): -42.23100 -6.504000 ymin,ymax (A): 4.829000 38.35600 zmin,zma (A): 17.16400 61.68000 x,y,z range (A): 35.72700 33.52700 44.51600 scale (grids/A): 2.399137 object centre (A): -24.36750 21.59250 39.42200 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.514006 assigned positive charge : 164.8092 centred at (gu) : 90.59103 88.96968 86.76282 assigned negative charge : -163.2951 centred at (gu) : 90.77434 88.34161 87.24967 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 53078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10352 grid for indexing accessible points = 1.400000 m= 22401 mr = 35974 m= 5062 mr = 17314 m= 630 mr = 3606 m= 31 mr = 387 m= 0 mr = 20 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2832 time to turn everything in is 0.4300000 number of dielectric boundary points 23901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8063 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) : 0.7997125 object centre at (A) : -24.36750 21.59250 39.42200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5424859E-02 1.8158911E-03 midg,1,midg; midg,igrid,midg -2.6055630E-02 2.3509301E-02 1,midg,midg; igrid,midg,midg 2.3826437E-02 1.9393882E-03 gauss-seidel spectral radius is 0.9989644 estimated iterations to convergence 246 setup time was (sec) 0.6900000 now iterating at: 15:00:38 rms-change max change #iterations 4.060141 208.7236 at 10iterations 2.093113 85.66841 at 20iterations 1.081778 37.80715 at 30iterations 0.5564242 18.48361 at 40iterations 0.2874612 9.266325 at 50iterations 0.1484338 5.097612 at 60iterations 7.6416112E-02 2.350603 at 70iterations 3.9534081E-02 1.311144 at 80iterations 2.0292250E-02 0.6790895 at 90iterations 1.0540619E-02 0.3551750 at 100iterations 5.4090219E-03 0.1783600 at 110iterations 2.7936576E-03 9.6435547E-02 at 120iterations finished qdiffx linear iterations at : 15:00:44 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 2.7936576E-03 9.6435547E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 15:00:44 6.921u 0.184s 0:07.44 95.4% 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 Sun Oct 9 2011 at 15:00:44 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.598706 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): -42.23100 -6.504000 ymin,ymax (A): 4.829000 38.35600 zmin,zma (A): 17.16400 61.68000 x,y,z range (A): 35.72700 33.52700 44.51600 scale (grids/A): 3.598706 object centre (A): -24.36750 21.59250 39.42200 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.514006 assigned positive charge : 164.8092 centred at (gu) : 90.88651 88.45457 85.14423 assigned negative charge : -163.2951 centred at (gu) : 91.16158 87.51239 85.87454 start vw surface at 0.1100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 121903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10352 grid for indexing accessible points = 1.400000 m= 66869 mr = 86328 m= 30045 mr = 55840 m= 9800 mr = 25258 m= 2392 mr = 7884 m= 425 mr = 1861 m= 52 mr = 327 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 10045 time to turn everything in is 1.260000 number of dielectric boundary points 53955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 8080 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) : 2.399137 object centre at (A) : -24.36750 21.59250 39.42200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1158893 8.5519105E-02 midg,1,midg; midg,igrid,midg -0.2270695 0.1182362 1,midg,midg; igrid,midg,midg 0.1585008 -5.5772722E-02 gauss-seidel spectral radius is 0.9993114 estimated iterations to convergence 301 setup time was (sec) 1.530000 now iterating at: 15:00:46 rms-change max change #iterations 8.511128 232.7399 at 10iterations 4.981817 117.3802 at 20iterations 2.912296 59.50465 at 30iterations 1.707572 34.50723 at 40iterations 0.9997935 21.20318 at 50iterations 0.5855835 11.90323 at 60iterations 0.3422931 6.570037 at 70iterations 0.2000733 3.961952 at 80iterations 0.1173167 2.133160 at 90iterations 6.8398230E-02 1.496069 at 100iterations 4.0052567E-02 0.7880859 at 110iterations 2.3481103E-02 0.4453373 at 120iterations 1.3698587E-02 0.2598591 at 130iterations 8.0264676E-03 0.1637936 at 140iterations 4.6980102E-03 8.8905811E-02 at 150iterations 2.7470558E-03 5.0830841E-02 at 160iterations 1.6084606E-03 2.9944420E-02 at 170iterations 9.4156864E-04 2.0099640E-02 at 180iterations finished qdiffx linear iterations at : 15:00:55 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 9.4156864E-04 2.0099640E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 15:00:56 11.220u 0.164s 0:11.91 95.5% 0+0k 0+0io 0pf+0w