Sat Oct 8 22:07:33 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 Sat Oct 8 2011 at 22:07:33 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6571054 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): -26.81900 26.03000 ymin,ymax (A): 7.867000 49.03300 zmin,zma (A): -12.78800 41.38900 x,y,z range (A): 52.84900 41.16600 54.17700 scale (grids/A): 0.6571054 object centre (A): -0.3945007 28.45000 14.30050 number of atom coordinates read : 2372 total number of charged atoms : 2237 net assigned charge : 11.00002 assigned positive charge : 346.6333 centred at (gu) : 90.39909 90.94437 91.35294 assigned negative charge : -335.6341 centred at (gu) : 90.41470 90.88855 91.32635 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6889 nv = 96 ne = 84 npr = 48351 no. pairs analyzed = 48351 no. exposed pairs = 3119 no. arc points = 22118 no. surface atoms = 1046 nbur = 1326 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3585 m= 0 mr = 46 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6391283E-08 3.9349146E-08 midg,1,midg; midg,igrid,midg 1.3934892E-08 4.1797637E-08 1,midg,midg; igrid,midg,midg 2.5925960E-08 2.5084555E-08 gauss-seidel spectral radius is 0.9879810 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 22:07:33 rms-change max change #iterations 0.1459420 22.48984 at 10iterations 1.5623533E-02 2.262356 at 20iterations 1.6400004E-03 0.2427483 at 30iterations 1.9028012E-04 2.4890900E-02 at 40iterations 3.0929274E-05 4.4417381E-03 at 50iterations finished qdiffx linear iterations at : 22:07:36 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.0929274E-05 4.4417381E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 22:07:37 3.561u 0.182s 0:04.01 93.2% 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 Sat Oct 8 2011 at 22:07:37 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.971316 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): -26.81900 26.03000 ymin,ymax (A): 7.867000 49.03300 zmin,zma (A): -12.78800 41.38900 x,y,z range (A): 52.84900 41.16600 54.17700 scale (grids/A): 1.971316 object centre (A): -0.3945007 28.45000 14.30050 number of atom coordinates read : 2372 total number of charged atoms : 2237 net assigned charge : 11.00002 assigned positive charge : 346.6333 centred at (gu) : 91.19698 92.83276 94.05840 assigned negative charge : -335.6341 centred at (gu) : 91.24401 92.66570 93.97903 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22118 grid for indexing accessible points = 1.400000 m= 26099 mr = 49554 m= 4369 mr = 18667 m= 297 mr = 2801 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 362 time to turn everything in is 0.3800000 number of dielectric boundary points 33394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17680 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) : 0.6571054 object centre at (A) : -0.3945007 28.45000 14.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0137414E-02 2.6089048E-02 midg,1,midg; midg,igrid,midg 5.1010726E-03 3.2458134E-02 1,midg,midg; igrid,midg,midg 5.7061292E-02 5.5496577E-02 gauss-seidel spectral radius is 0.9987049 estimated iterations to convergence 220 setup time was (sec) 0.6200000 now iterating at: 22:07:38 rms-change max change #iterations 4.215487 191.4944 at 10iterations 2.009362 71.50526 at 20iterations 0.9560305 31.87152 at 30iterations 0.4578620 15.23941 at 40iterations 0.2182724 6.583098 at 50iterations 0.1039143 3.437356 at 60iterations 4.9517926E-02 1.581770 at 70iterations 2.3691244E-02 0.7145939 at 80iterations 1.1362746E-02 0.3809395 at 90iterations 5.4006232E-03 0.1684589 at 100iterations 2.5894057E-03 7.6862335E-02 at 110iterations 1.2330191E-03 3.7017822E-02 at 120iterations finished qdiffx linear iterations at : 22:07:45 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 1.2330191E-03 3.7017822E-02 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 22:07:46 8.410u 0.230s 0:08.93 96.7% 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 Sat Oct 8 2011 at 22:07:46 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.956975 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): -26.81900 26.03000 ymin,ymax (A): 7.867000 49.03300 zmin,zma (A): -12.78800 41.38900 x,y,z range (A): 52.84900 41.16600 54.17700 scale (grids/A): 2.956975 object centre (A): -0.3945007 28.45000 14.30050 number of atom coordinates read : 2372 total number of charged atoms : 2237 net assigned charge : 11.00002 assigned positive charge : 346.6333 centred at (gu) : 91.79538 94.24892 96.08764 assigned negative charge : -335.6341 centred at (gu) : 91.86603 93.99857 95.96859 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 170681 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22118 grid for indexing accessible points = 1.400000 m= 83853 mr = 120932 m= 30745 mr = 67054 m= 7962 mr = 24365 m= 1330 mr = 6004 m= 96 mr = 929 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1212 time to turn everything in is 0.9900000 number of dielectric boundary points 75346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 17896 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) : 1.971316 object centre at (A) : -0.3945007 28.45000 14.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4944482 0.2692871 midg,1,midg; midg,igrid,midg 2.5442742E-02 0.3219060 1,midg,midg; igrid,midg,midg 0.6493268 0.5435176 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 1.260000 now iterating at: 22:07:47 rms-change max change #iterations 9.844752 413.2830 at 10iterations 5.817837 126.5286 at 20iterations 3.418028 85.36764 at 30iterations 2.006212 44.89960 at 40iterations 1.174442 23.26278 at 50iterations 0.6878759 15.55344 at 60iterations 0.4008364 7.332935 at 70iterations 0.2339435 4.127663 at 80iterations 0.1364553 2.482737 at 90iterations 7.9404250E-02 1.536522 at 100iterations 4.6133708E-02 0.8440423 at 110iterations 2.6880102E-02 0.5102358 at 120iterations 1.5627356E-02 0.3314037 at 130iterations 9.0859709E-03 0.1601353 at 140iterations 5.2845129E-03 0.1028194 at 150iterations 3.0693419E-03 5.7330132E-02 at 160iterations 1.7837173E-03 3.2958984E-02 at 170iterations 1.0438523E-03 2.2464752E-02 at 180iterations finished qdiffx linear iterations at : 22:08:00 total time elapsed so far: 13.72000 # loops : 180 mean,max change (kT/e) : 1.0438523E-03 2.2464752E-02 energy calculations done at 13.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 22:08:00 13.857u 0.239s 0:14.36 98.0% 0+0k 0+0io 0pf+0w