Tue Oct 11 08:33:31 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+sph.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 = amb.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 Tue Oct 11 2011 at 08:33:31 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6622147 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): -8.274000 40.59400 ymin,ymax (A): -26.28700 22.22900 zmin,zma (A): -9.873000 43.88600 x,y,z range (A): 48.86800 48.51600 53.75900 scale (grids/A): 0.6622147 object centre (A): 16.16000 -2.028999 17.00650 number of atom coordinates read : 2708 total number of charged atoms : 2556 net assigned charge : 2.140015 assigned positive charge : 407.9408 centred at (gu) : 89.62682 90.24364 88.67271 assigned negative charge : -405.8014 centred at (gu) : 89.93096 90.07680 88.63987 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7867 nv = 96 ne = 84 npr = 55770 no. pairs analyzed = 55770 no. exposed pairs = 3324 no. arc points = 23042 no. surface atoms = 1121 nbur = 1587 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4450 m= 4 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3200000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2286 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1957109E-09 9.7492503E-09 midg,1,midg; midg,igrid,midg -2.9883676E-08 4.3655870E-08 1,midg,midg; igrid,midg,midg 7.5763772E-08 -5.8218166E-08 gauss-seidel spectral radius is 0.9881868 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 08:33:32 rms-change max change #iterations 0.1737251 22.77716 at 10iterations 1.9150803E-02 2.498592 at 20iterations 2.0539826E-03 0.2508125 at 30iterations 2.3284784E-04 2.9336929E-02 at 40iterations 2.9983814E-05 4.9495697E-03 at 50iterations finished qdiffx linear iterations at : 08:33:36 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 2.9983814E-05 4.9495697E-03 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 08:33:36 4.718u 0.381s 0:05.39 94.4% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 08:33:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.986644 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): -8.274000 40.59400 ymin,ymax (A): -26.28700 22.22900 zmin,zma (A): -9.873000 43.88600 x,y,z range (A): 48.86800 48.51600 53.75900 scale (grids/A): 1.986644 object centre (A): 16.16000 -2.028999 17.00650 number of atom coordinates read : 2708 total number of charged atoms : 2556 net assigned charge : 2.140015 assigned positive charge : 407.9408 centred at (gu) : 88.87961 90.73034 86.01768 assigned negative charge : -405.8014 centred at (gu) : 89.79277 90.23004 85.91936 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23042 grid for indexing accessible points = 1.400000 m= 31848 mr = 60064 m= 5467 mr = 23657 m= 415 mr = 3502 m= 6 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 599 time to turn everything in is 0.6900000 number of dielectric boundary points 35289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20147 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) : 0.6622147 object centre at (A) : 16.16000 -2.028999 17.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5345262E-02 -2.8377229E-02 midg,1,midg; midg,igrid,midg -1.5250988E-02 4.3256857E-02 1,midg,midg; igrid,midg,midg 8.6320214E-02 -1.3711050E-02 gauss-seidel spectral radius is 0.9987506 estimated iterations to convergence 224 setup time was (sec) 0.9900000 now iterating at: 08:33:40 rms-change max change #iterations 4.735598 212.2182 at 10iterations 2.302699 74.15311 at 20iterations 1.111657 43.22456 at 30iterations 0.5398666 16.41690 at 40iterations 0.2620378 7.700275 at 50iterations 0.1269567 3.890907 at 60iterations 6.1391037E-02 1.788373 at 70iterations 2.9838800E-02 0.8105412 at 80iterations 1.4472079E-02 0.4483261 at 90iterations 7.0095770E-03 0.2081032 at 100iterations 3.4099102E-03 0.1009941 at 110iterations 1.6561662E-03 4.8568726E-02 at 120iterations finished qdiffx linear iterations at : 08:33:51 total time elapsed so far: 11.99000 # loops : 120 mean,max change (kT/e) : 1.6561662E-03 4.8568726E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 08:33:51 12.184u 0.475s 0:15.02 84.2% 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 Tue Oct 11 2011 at 08:33:51 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.979966 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): -8.274000 40.59400 ymin,ymax (A): -26.28700 22.22900 zmin,zma (A): -9.873000 43.88600 x,y,z range (A): 48.86800 48.51600 53.75900 scale (grids/A): 2.979966 object centre (A): 16.16000 -2.028999 17.00650 number of atom coordinates read : 2708 total number of charged atoms : 2556 net assigned charge : 2.140015 assigned positive charge : 407.9408 centred at (gu) : 88.31952 91.09547 84.02636 assigned negative charge : -405.8014 centred at (gu) : 89.68916 90.34501 83.87885 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 196443 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23042 grid for indexing accessible points = 1.400000 m= 102113 mr = 145075 m= 38161 mr = 84268 m= 10003 mr = 30837 m= 1656 mr = 7614 m= 116 mr = 1096 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 1987 time to turn everything in is 1.850000 number of dielectric boundary points 79555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 20443 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) : 1.986644 object centre at (A) : 16.16000 -2.028999 17.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1463697 -0.3463549 midg,1,midg; midg,igrid,midg -0.1490638 0.4924665 1,midg,midg; igrid,midg,midg 0.7389246 -9.1678254E-02 gauss-seidel spectral radius is 0.9992872 estimated iterations to convergence 296 setup time was (sec) 2.200000 now iterating at: 08:33:54 rms-change max change #iterations 10.87403 383.0682 at 10iterations 6.391608 130.7479 at 20iterations 3.757104 76.86139 at 30iterations 2.200320 37.42517 at 40iterations 1.290361 26.80115 at 50iterations 0.7555823 14.61156 at 60iterations 0.4410808 7.347340 at 70iterations 0.2568058 4.664703 at 80iterations 0.1501957 2.704613 at 90iterations 8.7411955E-02 1.451101 at 100iterations 5.0890595E-02 0.8671112 at 110iterations 2.9677195E-02 0.4969387 at 120iterations 1.7279506E-02 0.2832205 at 130iterations 1.0067819E-02 0.1892090 at 140iterations 5.8825174E-03 0.1099854 at 150iterations 3.4435869E-03 5.9745789E-02 at 160iterations 2.0225402E-03 3.3161163E-02 at 170iterations 1.1963521E-03 1.9802094E-02 at 180iterations finished qdiffx linear iterations at : 08:34:12 total time elapsed so far: 19.86000 # loops : 180 mean,max change (kT/e) : 1.1963521E-03 1.9802094E-02 energy calculations done at 19.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.04000 DelPhi exited at 08:34:12 20.044u 0.477s 0:20.97 97.8% 0+0k 0+0io 0pf+0w