Sat Oct 8 18:33:25 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 Sat Oct 8 2011 at 18:33:25 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6216168 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): -31.48600 17.44400 ymin,ymax (A): -23.54000 22.89600 zmin,zma (A): -12.52300 44.74700 x,y,z range (A): 48.93000 46.43600 57.27000 scale (grids/A): 0.6216168 object centre (A): -7.021000 -0.3219995 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.38054 89.23537 89.84386 assigned negative charge : -387.9385 centred at (gu) : 88.27345 89.27132 89.72569 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 55175 no. pairs analyzed = 55175 no. exposed pairs = 2935 no. arc points = 21127 no. surface atoms = 991 nbur = 1603 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3693 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 227 time to turn everything in is 0.3500000 number of dielectric boundary points 3096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2086 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8014 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0569429E-09 1.1131344E-08 midg,1,midg; midg,igrid,midg 6.9899677E-09 8.0659551E-10 1,midg,midg; igrid,midg,midg -5.9929537E-09 7.5654247E-09 gauss-seidel spectral radius is 0.9865907 estimated iterations to convergence 71 setup time was (sec) 0.6200000 now iterating at: 18:33:26 rms-change max change #iterations 0.1309592 19.78632 at 10iterations 1.1884457E-02 1.907580 at 20iterations 1.1030085E-03 0.1602116 at 30iterations 1.0363058E-04 1.4890671E-02 at 40iterations 9.7112797E-06 1.4705658E-03 at 50iterations finished qdiffx linear iterations at : 18:33:29 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 9.7112797E-06 1.4705658E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 18:33:30 4.079u 0.254s 0:04.59 94.1% 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 Sat Oct 8 2011 at 18:33:30 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.864851 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): -31.48600 17.44400 ymin,ymax (A): -23.54000 22.89600 zmin,zma (A): -12.52300 44.74700 x,y,z range (A): 48.93000 46.43600 57.27000 scale (grids/A): 1.864851 object centre (A): -7.021000 -0.3219995 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.14130 87.70573 89.53111 assigned negative charge : -387.9385 centred at (gu) : 84.82022 87.81365 89.17681 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21127 grid for indexing accessible points = 1.400000 m= 24650 mr = 49549 m= 3549 mr = 18471 m= 207 mr = 2267 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 8666 time to turn everything in is 0.6300000 number of dielectric boundary points 28523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19196 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) : 0.6216168 object centre at (A) : -7.021000 -0.3219995 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5329968E-02 3.0885402E-02 midg,1,midg; midg,igrid,midg 1.2466149E-02 2.2402883E-03 1,midg,midg; igrid,midg,midg -9.7560789E-03 3.4842137E-02 gauss-seidel spectral radius is 0.9985698 estimated iterations to convergence 210 setup time was (sec) 0.9200000 now iterating at: 18:33:31 rms-change max change #iterations 4.048425 174.0165 at 10iterations 1.858950 64.17743 at 20iterations 0.8587933 33.46403 at 30iterations 0.3931629 14.48911 at 40iterations 0.1817798 6.315079 at 50iterations 8.3556019E-02 2.844807 at 60iterations 3.8544372E-02 1.266563 at 70iterations 1.7755279E-02 0.5606279 at 80iterations 8.1516225E-03 0.2493773 at 90iterations 3.7706059E-03 0.1236153 at 100iterations 1.7286015E-03 5.4029465E-02 at 110iterations 7.9850090E-04 2.5008202E-02 at 120iterations finished qdiffx linear iterations at : 18:33:39 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 7.9850090E-04 2.5008202E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 18:33:40 9.326u 0.293s 0:09.88 97.2% 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 Sat Oct 8 2011 at 18:33:40 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.797276 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): -31.48600 17.44400 ymin,ymax (A): -23.54000 22.89600 zmin,zma (A): -12.52300 44.74700 x,y,z range (A): 48.93000 46.43600 57.27000 scale (grids/A): 2.797276 object centre (A): -7.021000 -0.3219995 16.11200 number of atom coordinates read : 2594 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 82.71171 86.55849 89.29663 assigned negative charge : -387.9385 centred at (gu) : 82.23037 86.72038 88.76528 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 163290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21127 grid for indexing accessible points = 1.400000 m= 81656 mr = 119892 m= 28044 mr = 67780 m= 6359 mr = 22716 m= 881 mr = 4873 m= 52 mr = 658 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 29294 time to turn everything in is 1.570000 number of dielectric boundary points 64331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19595 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) : 1.864851 object centre at (A) : -7.021000 -0.3219995 16.11200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1266092E-02 0.3721007 midg,1,midg; midg,igrid,midg 0.1509214 2.5767185E-02 1,midg,midg; igrid,midg,midg -8.2597516E-02 0.4531683 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.880000 now iterating at: 18:33:42 rms-change max change #iterations 9.521296 336.6622 at 10iterations 5.447000 116.7130 at 20iterations 3.105187 59.44788 at 30iterations 1.767132 37.45229 at 40iterations 1.006081 18.30809 at 50iterations 0.5721534 10.50867 at 60iterations 0.3254492 6.265373 at 70iterations 0.1851235 3.207987 at 80iterations 0.1052544 1.895333 at 90iterations 5.9749007E-02 1.186501 at 100iterations 3.3913121E-02 0.6628952 at 110iterations 1.9337740E-02 0.3592300 at 120iterations 1.0985668E-02 0.1976852 at 130iterations 6.2292051E-03 0.1176529 at 140iterations 3.5459795E-03 6.2206268E-02 at 150iterations 2.0123895E-03 3.6769867E-02 at 160iterations 1.1435201E-03 2.2850037E-02 at 170iterations 6.5021717E-04 1.2174606E-02 at 180iterations finished qdiffx linear iterations at : 18:33:55 total time elapsed so far: 15.30000 # loops : 180 mean,max change (kT/e) : 6.5021717E-04 1.2174606E-02 energy calculations done at 15.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.48000 DelPhi exited at 18:33:56 15.484u 0.306s 0:16.05 98.3% 0+0k 0+0io 0pf+0w