Sun Oct 9 22:48:38 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 22:48:38 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 !!! WARNING: SEP 108 has a net charge of -0.4750 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: 0.6525525 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): 12.09700 66.12500 ymin,ymax (A): -11.99500 31.06900 zmin,zma (A): -11.35700 43.19800 x,y,z range (A): 54.02800 43.06400 54.55500 scale (grids/A): 0.6525525 object centre (A): 39.11100 9.537000 15.92050 number of atom coordinates read : 2185 total number of charged atoms : 2044 net assigned charge : 4.025002 assigned positive charge : 324.4886 centred at (gu) : 89.12621 91.75874 90.22759 assigned negative charge : -320.4639 centred at (gu) : 89.32446 91.67247 90.01891 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6373 nv = 96 ne = 84 npr = 42595 no. pairs analyzed = 42595 no. exposed pairs = 2863 no. arc points = 20334 no. surface atoms = 969 nbur = 1216 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3369 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1952 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7440 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9824229E-08 3.6962291E-08 midg,1,midg; midg,igrid,midg -2.5463021E-09 2.8001871E-08 1,midg,midg; igrid,midg,midg 4.0799087E-08 -1.6003591E-08 gauss-seidel spectral radius is 0.9877996 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 22:48:39 rms-change max change #iterations 0.1433949 23.11429 at 10iterations 1.4879602E-02 2.111626 at 20iterations 1.5611919E-03 0.2190247 at 30iterations 2.0510529E-04 3.4763336E-02 at 40iterations 5.5481469E-05 1.0882854E-02 at 50iterations finished qdiffx linear iterations at : 22:48:41 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 5.5481469E-05 1.0882854E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 22:48:42 3.248u 0.222s 0:03.77 91.7% 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 22:48:42 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 !!! WARNING: SEP 108 has a net charge of -0.4750 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: 1.957657 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): 12.09700 66.12500 ymin,ymax (A): -11.99500 31.06900 zmin,zma (A): -11.35700 43.19800 x,y,z range (A): 54.02800 43.06400 54.55500 scale (grids/A): 1.957657 object centre (A): 39.11100 9.537000 15.92050 number of atom coordinates read : 2185 total number of charged atoms : 2044 net assigned charge : 4.025002 assigned positive charge : 324.4886 centred at (gu) : 87.37828 95.27608 90.68237 assigned negative charge : -320.4639 centred at (gu) : 87.97353 95.01746 90.05663 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20334 grid for indexing accessible points = 1.400000 m= 24167 mr = 46286 m= 4113 mr = 17545 m= 308 mr = 2676 m= 2 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 30524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16133 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) : 0.6525525 object centre at (A) : 39.11100 9.537000 15.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5913418E-02 1.1615971E-02 midg,1,midg; midg,igrid,midg -1.0117049E-02 1.0775699E-02 1,midg,midg; igrid,midg,midg 2.9876396E-02 1.9272240E-02 gauss-seidel spectral radius is 0.9986720 estimated iterations to convergence 217 setup time was (sec) 0.7800000 now iterating at: 22:48:43 rms-change max change #iterations 4.020312 208.1579 at 10iterations 1.905781 79.10095 at 20iterations 0.9042050 28.82295 at 30iterations 0.4256413 15.11466 at 40iterations 0.2011781 6.787654 at 50iterations 9.5558427E-02 3.561207 at 60iterations 4.5137234E-02 1.435810 at 70iterations 2.1389356E-02 0.7398686 at 80iterations 1.0185353E-02 0.3541298 at 90iterations 4.8789741E-03 0.1764698 at 100iterations 2.3911952E-03 8.2523346E-02 at 110iterations 1.2181634E-03 4.7609329E-02 at 120iterations finished qdiffx linear iterations at : 22:48:49 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.2181634E-03 4.7609329E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 22:48:49 7.055u 0.228s 0:07.70 94.4% 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 22:48:50 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2185 !!! WARNING: SEP 108 has a net charge of -0.4750 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: 2.936486 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): 12.09700 66.12500 ymin,ymax (A): -11.99500 31.06900 zmin,zma (A): -11.35700 43.19800 x,y,z range (A): 54.02800 43.06400 54.55500 scale (grids/A): 2.936486 object centre (A): 39.11100 9.537000 15.92050 number of atom coordinates read : 2185 total number of charged atoms : 2044 net assigned charge : 4.025002 assigned positive charge : 324.4886 centred at (gu) : 86.06734 97.91396 91.02363 assigned negative charge : -320.4639 centred at (gu) : 86.96030 97.52616 90.08479 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 158487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20334 grid for indexing accessible points = 1.400000 m= 78266 mr = 112361 m= 28275 mr = 63425 m= 7402 mr = 22505 m= 1282 mr = 5585 m= 118 mr = 922 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 68959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 16352 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) : 1.957657 object centre at (A) : 39.11100 9.537000 15.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7229925E-02 -7.8151338E-02 midg,1,midg; midg,igrid,midg -0.1616587 0.1017021 1,midg,midg; igrid,midg,midg 0.1525153 0.5107101 gauss-seidel spectral radius is 0.9992667 estimated iterations to convergence 291 setup time was (sec) 1.520000 now iterating at: 22:48:51 rms-change max change #iterations 9.455191 398.1187 at 10iterations 5.558167 168.6295 at 20iterations 3.251168 74.63667 at 30iterations 1.897333 40.26820 at 40iterations 1.104497 24.87333 at 50iterations 0.6410241 12.95364 at 60iterations 0.3710620 8.285267 at 70iterations 0.2154463 4.130478 at 80iterations 0.1246498 2.542165 at 90iterations 7.2209045E-02 1.516951 at 100iterations 4.1620240E-02 0.7829018 at 110iterations 2.4103381E-02 0.4953446 at 120iterations 1.3902174E-02 0.2688291 at 130iterations 8.0192126E-03 0.1522660 at 140iterations 4.6449965E-03 9.8114967E-02 at 150iterations 2.6740525E-03 5.2789688E-02 at 160iterations 1.5397317E-03 2.7960777E-02 at 170iterations 8.9016766E-04 1.6982079E-02 at 180iterations finished qdiffx linear iterations at : 22:49:01 total time elapsed so far: 11.73000 # loops : 180 mean,max change (kT/e) : 8.9016766E-04 1.6982079E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 22:49:02 11.897u 0.256s 0:12.44 97.5% 0+0k 0+0io 0pf+0w