Tue Oct 11 03:17:07 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 03:17:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6032467 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): -12.82700 46.18700 ymin,ymax (A): -2.775000 47.78100 zmin,zma (A): -13.07100 39.72800 x,y,z range (A): 59.01400 50.55600 52.79900 scale (grids/A): 0.6032467 object centre (A): 16.68000 22.50300 13.32850 number of atom coordinates read : 2678 total number of charged atoms : 2559 net assigned charge : 4.500017 assigned positive charge : 398.0525 centred at (gu) : 87.67565 90.31982 90.59391 assigned negative charge : -393.5536 centred at (gu) : 87.59593 90.30588 90.52766 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6777 nv = 96 ne = 84 npr = 52220 no. pairs analyzed = 52220 no. exposed pairs = 3867 no. arc points = 27848 no. surface atoms = 1280 nbur = 1398 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3277 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2691 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8199 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3801857E-10 5.5620495E-09 midg,1,midg; midg,igrid,midg 1.5191636E-09 2.9622429E-09 1,midg,midg; igrid,midg,midg -1.9495852E-09 3.2224157E-09 gauss-seidel spectral radius is 0.9857985 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 03:17:09 rms-change max change #iterations 0.1066504 18.44322 at 10iterations 9.5545864E-03 1.459835 at 20iterations 1.2064680E-03 0.1904564 at 30iterations 3.2779627E-04 5.1911354E-02 at 40iterations 1.1230532E-04 1.8146515E-02 at 50iterations finished qdiffx linear iterations at : 03:17:11 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.1230532E-04 1.8146515E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 03:17:12 3.191u 0.161s 0:03.94 85.0% 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 Tue Oct 11 2011 at 03:17:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.809740 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): -12.82700 46.18700 ymin,ymax (A): -2.775000 47.78100 zmin,zma (A): -13.07100 39.72800 x,y,z range (A): 59.01400 50.55600 52.79900 scale (grids/A): 1.809740 object centre (A): 16.68000 22.50300 13.32850 number of atom coordinates read : 2678 total number of charged atoms : 2559 net assigned charge : 4.500017 assigned positive charge : 398.0525 centred at (gu) : 83.02625 90.95873 91.78102 assigned negative charge : -393.5536 centred at (gu) : 82.78767 90.91755 91.58288 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27848 grid for indexing accessible points = 1.400000 m= 25742 mr = 46688 m= 3891 mr = 17603 m= 196 mr = 2111 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 133 time to turn everything in is 0.5100000 number of dielectric boundary points 35503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19999 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) : 0.6032467 object centre at (A) : 16.68000 22.50300 13.32850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3820588E-03 2.2591688E-02 midg,1,midg; midg,igrid,midg -2.0461600E-02 7.5700944E-03 1,midg,midg; igrid,midg,midg -2.3793424E-02 1.0302449E-03 gauss-seidel spectral radius is 0.9985282 estimated iterations to convergence 207 setup time was (sec) 0.7800000 now iterating at: 03:17:13 rms-change max change #iterations 3.887729 182.3548 at 10iterations 1.763087 61.60609 at 20iterations 0.7987657 26.99174 at 30iterations 0.3629872 11.58053 at 40iterations 0.1652446 5.658084 at 50iterations 7.5036526E-02 2.536533 at 60iterations 3.4200996E-02 1.306024 at 70iterations 1.5627710E-02 0.4758625 at 80iterations 7.2079860E-03 0.2680359 at 90iterations 3.3650096E-03 0.1310024 at 100iterations 1.6185100E-03 6.5286636E-02 at 110iterations 8.1013713E-04 2.9116631E-02 at 120iterations finished qdiffx linear iterations at : 03:17:18 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 8.1013713E-04 2.9116631E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 03:17:19 6.870u 0.156s 0:07.30 96.1% 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 Tue Oct 11 2011 at 03:17:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 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: 2.714610 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): -12.82700 46.18700 ymin,ymax (A): -2.775000 47.78100 zmin,zma (A): -13.07100 39.72800 x,y,z range (A): 59.01400 50.55600 52.79900 scale (grids/A): 2.714610 object centre (A): 16.68000 22.50300 13.32850 number of atom coordinates read : 2678 total number of charged atoms : 2559 net assigned charge : 4.500017 assigned positive charge : 398.0525 centred at (gu) : 79.53917 91.43803 92.67147 assigned negative charge : -393.5536 centred at (gu) : 79.18148 91.37629 92.37435 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 166360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27848 grid for indexing accessible points = 1.400000 m= 82131 mr = 114050 m= 29485 mr = 64064 m= 6608 mr = 22281 m= 839 mr = 4556 m= 47 mr = 479 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 501 time to turn everything in is 1.270000 number of dielectric boundary points 80030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20471 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) : 1.809740 object centre at (A) : 16.68000 22.50300 13.32850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2370381 0.2466643 midg,1,midg; midg,igrid,midg -0.2994127 0.1054959 1,midg,midg; igrid,midg,midg -0.3453605 -0.1678142 gauss-seidel spectral radius is 0.9992556 estimated iterations to convergence 289 setup time was (sec) 1.550000 now iterating at: 03:17:21 rms-change max change #iterations 9.725723 352.3462 at 10iterations 5.823090 189.6589 at 20iterations 3.441413 90.76697 at 30iterations 2.017354 47.54809 at 40iterations 1.178798 23.92314 at 50iterations 0.6862826 14.73098 at 60iterations 0.3993071 8.190636 at 70iterations 0.2310888 5.042707 at 80iterations 0.1337718 2.776789 at 90iterations 7.6978117E-02 1.569519 at 100iterations 4.4596158E-02 0.8847046 at 110iterations 2.5716484E-02 0.5099182 at 120iterations 1.4795605E-02 0.2821312 at 130iterations 8.5512120E-03 0.1986027 at 140iterations 4.9555269E-03 9.2658997E-02 at 150iterations 2.8882704E-03 5.8982849E-02 at 160iterations 1.7039968E-03 3.1529903E-02 at 170iterations 1.0280686E-03 2.2823334E-02 at 180iterations finished qdiffx linear iterations at : 03:17:30 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 1.0280686E-03 2.2823334E-02 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 03:17:31 11.230u 0.160s 0:11.68 97.5% 0+0k 0+0io 0pf+0w