Mon Oct 10 09:44:09 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 Mon Oct 10 2011 at 09:44:09 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 = 2823 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5889457 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): -16.92200 35.94600 ymin,ymax (A): -64.03700 -4.888000 zmin,zma (A): -3.144000 57.30300 x,y,z range (A): 52.86800 59.14900 60.44700 scale (grids/A): 0.5889457 object centre (A): 9.511999 -34.46250 27.07950 number of atom coordinates read : 2823 total number of charged atoms : 2672 net assigned charge : 5.000016 assigned positive charge : 413.6930 centred at (gu) : 89.00422 89.42044 86.96783 assigned negative charge : -408.6934 centred at (gu) : 89.14500 89.28239 86.87937 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6495 nv = 96 ne = 84 npr = 55223 no. pairs analyzed = 55223 no. exposed pairs = 4260 no. arc points = 30729 no. surface atoms = 1403 nbur = 1420 mkacc time = 8.9999996E-02 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 = 1.484000 m= 335 mr = 2807 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3031 ## 306 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8190 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8799355E-09 1.9514532E-09 midg,1,midg; midg,igrid,midg -2.5535658E-09 4.5212385E-09 1,midg,midg; igrid,midg,midg 6.6070687E-09 -1.8021421E-09 gauss-seidel spectral radius is 0.9851176 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 09:44:10 rms-change max change #iterations 9.9752799E-02 19.45004 at 10iterations 7.9081831E-03 1.278407 at 20iterations 6.3667179E-04 9.9601746E-02 at 30iterations 5.4140797E-05 1.1383057E-02 at 40iterations 6.0618368E-06 8.8310242E-04 at 50iterations finished qdiffx linear iterations at : 09:44:12 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 6.0618368E-06 8.8310242E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 09:44:13 3.446u 0.181s 0:04.24 85.3% 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 Mon Oct 10 2011 at 09:44:13 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 = 2823 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.766837 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): -16.92200 35.94600 ymin,ymax (A): -64.03700 -4.888000 zmin,zma (A): -3.144000 57.30300 x,y,z range (A): 52.86800 59.14900 60.44700 scale (grids/A): 1.766837 object centre (A): 9.511999 -34.46250 27.07950 number of atom coordinates read : 2823 total number of charged atoms : 2672 net assigned charge : 5.000016 assigned positive charge : 413.6930 centred at (gu) : 87.01210 88.26070 80.90288 assigned negative charge : -408.6934 centred at (gu) : 87.43468 87.84686 80.63786 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30729 grid for indexing accessible points = 1.400000 m= 21906 mr = 42268 m= 3055 mr = 13734 m= 130 mr = 1397 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 37160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20780 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) : 0.5889457 object centre at (A) : 9.511999 -34.46250 27.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7589120E-03 4.2188680E-03 midg,1,midg; midg,igrid,midg 1.8295627E-02 4.6739630E-02 1,midg,midg; igrid,midg,midg 1.6361296E-02 -9.2843710E-04 gauss-seidel spectral radius is 0.9984545 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 09:44:14 rms-change max change #iterations 3.761320 154.2974 at 10iterations 1.671463 60.77400 at 20iterations 0.7433722 25.02645 at 30iterations 0.3291182 12.76554 at 40iterations 0.1468500 5.376339 at 50iterations 6.5227121E-02 2.275661 at 60iterations 2.9133627E-02 0.9334651 at 70iterations 1.2927867E-02 0.4780674 at 80iterations 5.7599582E-03 0.1925440 at 90iterations 2.5586586E-03 0.1031506 at 100iterations 1.1426185E-03 4.0159583E-02 at 110iterations 5.0844491E-04 1.6624451E-02 at 120iterations finished qdiffx linear iterations at : 09:44:21 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 5.0844491E-04 1.6624451E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 09:44:22 7.854u 0.195s 0:08.33 96.5% 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 Mon Oct 10 2011 at 09:44:22 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 = 2823 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.650255 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): -16.92200 35.94600 ymin,ymax (A): -64.03700 -4.888000 zmin,zma (A): -3.144000 57.30300 x,y,z range (A): 52.86800 59.14900 60.44700 scale (grids/A): 2.650255 object centre (A): 9.511999 -34.46250 27.07950 number of atom coordinates read : 2823 total number of charged atoms : 2672 net assigned charge : 5.000016 assigned positive charge : 413.6930 centred at (gu) : 85.51817 87.39100 76.35419 assigned negative charge : -408.6934 centred at (gu) : 86.15199 86.77025 75.95676 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30729 grid for indexing accessible points = 1.400000 m= 71669 mr = 104674 m= 23710 mr = 52964 m= 4962 mr = 16888 m= 497 mr = 2954 m= 21 mr = 217 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 83765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 21371 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) : 1.766837 object centre at (A) : 9.511999 -34.46250 27.07950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4586317E-02 6.3171357E-02 midg,1,midg; midg,igrid,midg 0.5872549 0.5280997 1,midg,midg; igrid,midg,midg 0.1389134 3.7356380E-02 gauss-seidel spectral radius is 0.9992356 estimated iterations to convergence 285 setup time was (sec) 1.140000 now iterating at: 09:44:23 rms-change max change #iterations 9.570930 300.2249 at 10iterations 5.671713 145.3565 at 20iterations 3.316235 93.63081 at 30iterations 1.930964 50.74103 at 40iterations 1.111711 28.79251 at 50iterations 0.6412516 15.12866 at 60iterations 0.3685098 9.808393 at 70iterations 0.2113347 4.945829 at 80iterations 0.1209131 2.718892 at 90iterations 6.9141209E-02 1.653601 at 100iterations 3.9591696E-02 0.8326664 at 110iterations 2.2520846E-02 0.4592590 at 120iterations 1.2834139E-02 0.2467213 at 130iterations 7.3044216E-03 0.1583452 at 140iterations 4.1629258E-03 8.9942813E-02 at 150iterations 2.3719040E-03 5.3135872E-02 at 160iterations 1.3497777E-03 2.8304577E-02 at 170iterations 7.7052595E-04 1.6234398E-02 at 180iterations finished qdiffx linear iterations at : 09:44:34 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 7.7052595E-04 1.6234398E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 09:44:35 12.728u 0.205s 0:13.24 97.5% 0+0k 0+0io 0pf+0w