Sun Oct 9 17:18:46 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 17:18:46 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5020 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5630239 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): 3.242000 64.91800 ymin,ymax (A): -8.584000 53.48200 zmin,zma (A): -1.207000 62.02300 x,y,z range (A): 61.67600 62.06600 63.23000 scale (grids/A): 0.5630239 object centre (A): 34.08000 22.44900 30.40800 number of atom coordinates read : 5020 total number of charged atoms : 4881 net assigned charge : -0.9649540 assigned positive charge : 775.7079 centred at (gu) : 88.35172 89.21785 89.17744 assigned negative charge : -776.6786 centred at (gu) : 88.23011 89.24058 89.14670 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10430 nv = 96 ne = 84 npr = 100984 no. pairs analyzed = 100984 no. exposed pairs = 6025 no. arc points = 40676 no. surface atoms = 2053 nbur = 2967 mkacc time = 0.2400000 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 = 1.512000 m= 494 mr = 5972 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4085 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 13628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8547958E-10 4.8477883E-10 midg,1,midg; midg,igrid,midg 5.1386362E-10 -4.5658421E-10 1,midg,midg; igrid,midg,midg -4.0705270E-09 1.6788655E-09 gauss-seidel spectral radius is 0.9838788 estimated iterations to convergence 65 setup time was (sec) 0.7400000 now iterating at: 17:18:47 rms-change max change #iterations 0.1189205 15.78074 at 10iterations 1.0602465E-02 1.317722 at 20iterations 2.6897725E-03 0.3040466 at 30iterations 1.2371168E-03 0.1323743 at 40iterations 6.0389331E-04 7.1353436E-02 at 50iterations finished qdiffx linear iterations at : 17:18:49 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 6.0389331E-04 7.1353436E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 17:18:50 3.589u 0.152s 0:04.01 93.0% 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 17:18:50 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5020 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.689072 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): 3.242000 64.91800 ymin,ymax (A): -8.584000 53.48200 zmin,zma (A): -1.207000 62.02300 x,y,z range (A): 61.67600 62.06600 63.23000 scale (grids/A): 1.689072 object centre (A): 34.08000 22.44900 30.40800 number of atom coordinates read : 5020 total number of charged atoms : 4881 net assigned charge : -0.9649540 assigned positive charge : 775.7079 centred at (gu) : 85.05395 87.65199 87.53066 assigned negative charge : -776.6786 centred at (gu) : 84.69044 87.72179 87.44026 start vw surface at 0.2200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 116270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40676 grid for indexing accessible points = 1.400000 m= 41216 mr = 84086 m= 5290 mr = 29860 m= 185 mr = 2862 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 46125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 37629 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) : 0.5630239 object centre at (A) : 34.08000 22.44900 30.40800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1031927E-02 -2.7705930E-02 midg,1,midg; midg,igrid,midg 1.5898254E-02 8.8614291E-03 1,midg,midg; igrid,midg,midg -2.7435660E-02 2.8314603E-02 gauss-seidel spectral radius is 0.9984944 estimated iterations to convergence 204 setup time was (sec) 1.140000 now iterating at: 17:18:51 rms-change max change #iterations 5.024286 164.4341 at 10iterations 2.260800 63.13252 at 20iterations 1.019789 30.32169 at 30iterations 0.4624674 12.69320 at 40iterations 0.2082996 5.659710 at 50iterations 9.4645575E-02 2.549254 at 60iterations 4.3186251E-02 1.165894 at 70iterations 2.0022405E-02 0.5542955 at 80iterations 9.6531091E-03 0.3002415 at 90iterations 5.0901575E-03 0.1457901 at 100iterations 3.0485021E-03 7.8594208E-02 at 110iterations 2.0835570E-03 5.2963257E-02 at 120iterations finished qdiffx linear iterations at : 17:18:58 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 2.0835570E-03 5.2963257E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 17:18:58 7.966u 0.174s 0:08.41 96.6% 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 17:18:58 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5020 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.533607 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): 3.242000 64.91800 ymin,ymax (A): -8.584000 53.48200 zmin,zma (A): -1.207000 62.02300 x,y,z range (A): 61.67600 62.06600 63.23000 scale (grids/A): 2.533607 object centre (A): 34.08000 22.44900 30.40800 number of atom coordinates read : 5020 total number of charged atoms : 4881 net assigned charge : -0.9649540 assigned positive charge : 775.7079 centred at (gu) : 82.58042 86.47758 86.29572 assigned negative charge : -776.6786 centred at (gu) : 82.03561 86.58255 86.16040 start vw surface at 0.2200000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 269801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40676 grid for indexing accessible points = 1.400000 m= 137641 mr = 204183 m= 45030 mr = 112165 m= 8774 mr = 35037 m= 802 mr = 6149 m= 29 mr = 417 m= 0 mr = 2 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 104124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 39011 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) : 1.689072 object centre at (A) : 34.08000 22.44900 30.40800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4637939 -0.6552087 midg,1,midg; midg,igrid,midg -2.0169854E-02 -1.6912548E-02 1,midg,midg; igrid,midg,midg -0.4383154 0.3251711 gauss-seidel spectral radius is 0.9992705 estimated iterations to convergence 292 setup time was (sec) 2.380000 now iterating at: 17:19:01 rms-change max change #iterations 12.62578 302.3492 at 10iterations 7.474854 147.7323 at 20iterations 4.406830 80.50637 at 30iterations 2.591042 48.35553 at 40iterations 1.516938 36.03493 at 50iterations 0.8853632 15.19077 at 60iterations 0.5152348 8.935699 at 70iterations 0.3000001 4.746674 at 80iterations 0.1742981 3.168671 at 90iterations 0.1012722 1.688271 at 100iterations 5.8679778E-02 0.9599075 at 110iterations 3.4212396E-02 0.5718136 at 120iterations 1.9955594E-02 0.3318024 at 130iterations 1.1787980E-02 0.1887207 at 140iterations 7.1109473E-03 0.1203346 at 150iterations 4.4521438E-03 6.9022179E-02 at 160iterations 2.9613278E-03 5.0308228E-02 at 170iterations 2.1245186E-03 3.4622192E-02 at 180iterations finished qdiffx linear iterations at : 17:19:12 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 2.1245186E-03 3.4622192E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 17:19:12 13.291u 0.191s 0:13.75 98.0% 0+0k 0+0io 0pf+0w