Wed Dec 28 11:03:34 PST 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 Wed Dec 28 2011 at 11:03:34 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6476377 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): -34.43000 5.651000 ymin,ymax (A): -5.010000 46.47700 zmin,zma (A): -31.10700 23.86200 x,y,z range (A): 40.08100 51.48700 54.96900 scale (grids/A): 0.6476377 object centre (A): -14.38950 20.73350 -3.622500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000007 assigned positive charge : 293.3999 centred at (gu) : 90.55434 87.43552 89.99989 assigned negative charge : -291.4002 centred at (gu) : 90.66964 87.29237 90.07192 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 5684 nv = 96 ne = 84 npr = 40475 no. pairs analyzed = 40475 no. exposed pairs = 2482 no. arc points = 17321 no. surface atoms = 840 nbur = 1130 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 287 mr = 3172 m= 2 mr = 27 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 0.3800000 number of dielectric boundary points 2774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1751873E-08 -3.6119667E-09 midg,1,midg; midg,igrid,midg -2.0180424E-08 1.1175435E-08 1,midg,midg; igrid,midg,midg 1.4466008E-08 -9.4113659E-09 gauss-seidel spectral radius is 0.9875907 estimated iterations to convergence 73 setup time was (sec) 0.6800000 now iterating at: 11:03:35 rms-change max change #iterations 0.1317543 18.92671 at 10iterations 1.3392516E-02 2.183811 at 20iterations 1.3604161E-03 0.2399063 at 30iterations 1.3920403E-04 2.1614075E-02 at 40iterations 1.4101188E-05 2.1133423E-03 at 50iterations finished qdiffx linear iterations at : 11:03:38 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.4101188E-05 2.1133423E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 11:03:39 4.190u 0.208s 0:04.75 92.4% 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 Wed Dec 28 2011 at 11:03:39 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.942913 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): -34.43000 5.651000 ymin,ymax (A): -5.010000 46.47700 zmin,zma (A): -31.10700 23.86200 x,y,z range (A): 40.08100 51.48700 54.96900 scale (grids/A): 1.942913 object centre (A): -14.38950 20.73350 -3.622500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000007 assigned positive charge : 293.3999 centred at (gu) : 91.66288 82.30640 89.99949 assigned negative charge : -291.4002 centred at (gu) : 92.00900 81.87745 90.21583 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 61299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17321 grid for indexing accessible points = 1.400000 m= 21605 mr = 42388 m= 3022 mr = 16261 m= 142 mr = 1866 m= 5 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2147 time to turn everything in is 0.6000000 number of dielectric boundary points 25520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 14489 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) : 0.6476377 object centre at (A) : -14.38950 20.73350 -3.622500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0173340E-02 4.2985428E-02 midg,1,midg; midg,igrid,midg -1.9598335E-02 3.2971170E-02 1,midg,midg; igrid,midg,midg 9.0790745E-03 -5.2210530E-03 gauss-seidel spectral radius is 0.9986106 estimated iterations to convergence 213 setup time was (sec) 0.9900000 now iterating at: 11:03:40 rms-change max change #iterations 3.788101 173.9624 at 10iterations 1.759707 68.84312 at 20iterations 0.8192587 31.78962 at 30iterations 0.3809448 14.34658 at 40iterations 0.1765597 6.564392 at 50iterations 8.2345985E-02 3.076632 at 60iterations 3.8192056E-02 1.448640 at 70iterations 1.7842636E-02 0.5888329 at 80iterations 8.2412399E-03 0.2974877 at 90iterations 3.8445159E-03 0.1297073 at 100iterations 1.7831011E-03 5.9113741E-02 at 110iterations 8.3202310E-04 3.0147552E-02 at 120iterations finished qdiffx linear iterations at : 11:03:48 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 8.3202310E-04 3.0147552E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 11:03:49 9.747u 0.199s 0:10.28 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 Wed Dec 28 2011 at 11:03:49 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.914370 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): -34.43000 5.651000 ymin,ymax (A): -5.010000 46.47700 zmin,zma (A): -31.10700 23.86200 x,y,z range (A): 40.08100 51.48700 54.96900 scale (grids/A): 2.914370 object centre (A): -14.38950 20.73350 -3.622500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000007 assigned positive charge : 293.3999 centred at (gu) : 92.49437 78.45962 89.99911 assigned negative charge : -291.4002 centred at (gu) : 93.01352 77.81616 90.32365 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 141902 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17321 grid for indexing accessible points = 1.400000 m= 71201 mr = 102647 m= 24400 mr = 58977 m= 5227 mr = 19977 m= 633 mr = 3849 m= 31 mr = 400 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 7266 time to turn everything in is 1.410000 number of dielectric boundary points 57533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 14704 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) : 1.942913 object centre at (A) : -14.38950 20.73350 -3.622500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4775882E-03 0.9515054 midg,1,midg; midg,igrid,midg -0.2209825 0.3596095 1,midg,midg; igrid,midg,midg 5.8054354E-02 -3.3674281E-02 gauss-seidel spectral radius is 0.9992380 estimated iterations to convergence 286 setup time was (sec) 1.770000 now iterating at: 11:03:51 rms-change max change #iterations 8.895710 530.4563 at 10iterations 5.128436 129.6180 at 20iterations 2.933136 72.94592 at 30iterations 1.672080 38.45325 at 40iterations 0.9565665 19.16506 at 50iterations 0.5437316 10.30591 at 60iterations 0.3106989 6.745495 at 70iterations 0.1766033 3.869993 at 80iterations 0.1007746 1.953690 at 90iterations 5.7225280E-02 1.289636 at 100iterations 3.2565299E-02 0.6609132 at 110iterations 1.8568542E-02 0.3444176 at 120iterations 1.0539914E-02 0.2113113 at 130iterations 5.9962170E-03 0.1141157 at 140iterations 3.4156162E-03 6.6357851E-02 at 150iterations 1.9383526E-03 4.0586472E-02 at 160iterations 1.1042573E-03 2.1152496E-02 at 170iterations 6.2774582E-04 1.1730671E-02 at 180iterations finished qdiffx linear iterations at : 11:04:04 total time elapsed so far: 14.47000 # loops : 180 mean,max change (kT/e) : 6.2774582E-04 1.1730671E-02 energy calculations done at 14.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.71000 DelPhi exited at 11:04:04 14.710u 0.231s 0:15.30 97.6% 0+0k 0+0io 0pf+0w