Sun Oct 9 06:14:29 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 Sun Oct 9 2011 at 06:14:29 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 = 1953 !!! WARNING: ASP 186 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6533070 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): 1.651000 44.02000 ymin,ymax (A): -8.893001 34.44300 zmin,zma (A): -24.90000 29.59200 x,y,z range (A): 42.36900 43.33600 54.49200 scale (grids/A): 0.6533070 object centre (A): 22.83550 12.77500 2.346000 number of atom coordinates read : 1953 total number of charged atoms : 1814 net assigned charge : 0.5000144 assigned positive charge : 288.6610 centred at (gu) : 90.04025 90.33681 88.17959 assigned negative charge : -288.1612 centred at (gu) : 89.85155 90.12334 88.07787 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5552 nv = 96 ne = 84 npr = 40572 no. pairs analyzed = 40572 no. exposed pairs = 2457 no. arc points = 17624 no. surface atoms = 831 nbur = 1122 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 2940 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3000000 number of dielectric boundary points 2881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1684 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6943762E-08 9.2957313E-09 midg,1,midg; midg,igrid,midg -2.3832399E-08 2.8960441E-08 1,midg,midg; igrid,midg,midg -2.2241858E-08 2.4231866E-08 gauss-seidel spectral radius is 0.9878002 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 06:14:29 rms-change max change #iterations 0.1348728 23.02572 at 10iterations 1.3826047E-02 2.246114 at 20iterations 1.4174874E-03 0.2042217 at 30iterations 1.4635402E-04 2.3933411E-02 at 40iterations 1.5110912E-05 2.4719238E-03 at 50iterations finished qdiffx linear iterations at : 06:14:32 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.5110912E-05 2.4719238E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 06:14:32 3.110u 0.136s 0:03.50 92.5% 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 06:14:32 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 = 1953 !!! WARNING: ASP 186 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.959921 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): 1.651000 44.02000 ymin,ymax (A): -8.893001 34.44300 zmin,zma (A): -24.90000 29.59200 x,y,z range (A): 42.36900 43.33600 54.49200 scale (grids/A): 1.959921 object centre (A): 22.83550 12.77500 2.346000 number of atom coordinates read : 1953 total number of charged atoms : 1814 net assigned charge : 0.5000144 assigned positive charge : 288.6610 centred at (gu) : 90.12090 91.01044 84.53889 assigned negative charge : -288.1612 centred at (gu) : 89.55482 90.37009 84.23391 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17624 grid for indexing accessible points = 1.400000 m= 21764 mr = 39917 m= 3774 mr = 16143 m= 213 mr = 2427 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 516 time to turn everything in is 0.4500000 number of dielectric boundary points 26328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14315 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) : 0.6533070 object centre at (A) : 22.83550 12.77500 2.346000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7493953E-02 3.0139735E-02 midg,1,midg; midg,igrid,midg -1.8328073E-02 3.4506071E-02 1,midg,midg; igrid,midg,midg -3.0465446E-02 1.8414164E-02 gauss-seidel spectral radius is 0.9986443 estimated iterations to convergence 215 setup time was (sec) 0.7400000 now iterating at: 06:14:33 rms-change max change #iterations 3.802765 179.1042 at 10iterations 1.775085 68.20087 at 20iterations 0.8317439 28.58294 at 30iterations 0.3896084 13.71670 at 40iterations 0.1828438 6.796761 at 50iterations 8.5971609E-02 2.852377 at 60iterations 4.0205866E-02 1.327578 at 70iterations 1.8848695E-02 0.6969690 at 80iterations 8.8313343E-03 0.2934895 at 90iterations 4.1548233E-03 0.1503401 at 100iterations 1.9534812E-03 7.0238113E-02 at 110iterations 9.1594440E-04 3.3687592E-02 at 120iterations finished qdiffx linear iterations at : 06:14:40 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 9.1594440E-04 3.3687592E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 06:14:40 7.389u 0.225s 0:07.99 95.1% 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 Sun Oct 9 2011 at 06:14:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASP 186 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.939881 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): 1.651000 44.02000 ymin,ymax (A): -8.893001 34.44300 zmin,zma (A): -24.90000 29.59200 x,y,z range (A): 42.36900 43.33600 54.49200 scale (grids/A): 2.939881 object centre (A): 22.83550 12.77500 2.346000 number of atom coordinates read : 1953 total number of charged atoms : 1814 net assigned charge : 0.5000144 assigned positive charge : 288.6610 centred at (gu) : 90.18143 91.51569 81.80824 assigned negative charge : -288.1612 centred at (gu) : 89.33223 90.55513 81.35080 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 136294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17624 grid for indexing accessible points = 1.400000 m= 68860 mr = 96588 m= 26530 mr = 56338 m= 6941 mr = 21603 m= 1012 mr = 5260 m= 67 mr = 690 m= 0 mr = 31 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1559 time to turn everything in is 1.150000 number of dielectric boundary points 59194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 14511 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) : 1.959921 object centre at (A) : 22.83550 12.77500 2.346000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8528072 0.3800904 midg,1,midg; midg,igrid,midg -0.1484201 0.3394821 1,midg,midg; igrid,midg,midg -0.2850814 0.1387494 gauss-seidel spectral radius is 0.9992491 estimated iterations to convergence 288 setup time was (sec) 1.450000 now iterating at: 06:14:42 rms-change max change #iterations 8.794133 421.9950 at 10iterations 5.055271 137.3620 at 20iterations 2.902879 60.77699 at 30iterations 1.655555 34.98801 at 40iterations 0.9472886 18.39653 at 50iterations 0.5422511 10.84437 at 60iterations 0.3093400 6.083747 at 70iterations 0.1766605 3.622726 at 80iterations 0.1007517 1.929923 at 90iterations 5.7475388E-02 1.214723 at 100iterations 3.2937430E-02 0.6225183 at 110iterations 1.8782461E-02 0.3706083 at 120iterations 1.0707363E-02 0.2121964 at 130iterations 6.1105755E-03 0.1266804 at 140iterations 3.4866545E-03 7.2716713E-02 at 150iterations 1.9937062E-03 4.0254593E-02 at 160iterations 1.1370014E-03 2.4383068E-02 at 170iterations 6.4703356E-04 1.4064789E-02 at 180iterations finished qdiffx linear iterations at : 06:14:52 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 6.4703356E-04 1.4064789E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 06:14:53 11.878u 0.225s 0:12.38 97.6% 0+0k 0+0io 0pf+0w