Wed Dec 21 14:22:31 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 21 2011 at 14:22:34 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6086094 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 0.6086094 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2260 centred at (gu) : 90.27914 90.34502 89.59123 assigned negative charge : -290.2263 centred at (gu) : 90.28324 90.46033 89.43827 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4895 nv = 96 ne = 84 npr = 40054 no. pairs analyzed = 40054 no. exposed pairs = 2481 no. arc points = 17575 no. surface atoms = 840 nbur = 1124 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 217 mr = 2649 m= 0 mr = 9 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2400000 number of dielectric boundary points 2454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1897 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7807704E-09 5.9407386E-09 midg,1,midg; midg,igrid,midg 4.8282049E-09 -3.2186664E-09 1,midg,midg; igrid,midg,midg 1.2455580E-09 1.0969645E-09 gauss-seidel spectral radius is 0.9859703 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 14:22:35 rms-change max change #iterations 0.1001722 17.52420 at 10iterations 8.7159397E-03 1.510872 at 20iterations 7.5601228E-04 0.1221137 at 30iterations 6.6159519E-05 1.4760017E-02 at 40iterations 5.8249107E-06 9.9182129E-04 at 50iterations finished qdiffx linear iterations at : 14:22:41 total time elapsed so far: 5.830000 # loops : 50 mean,max change (kT/e) : 5.8249107E-06 9.9182129E-04 energy calculations done at 5.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.020000 DelPhi exited at 14:22:46 6.022u 0.439s 0:13.15 49.0% 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 21 2011 at 14:22:49 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.825828 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 1.825828 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2260 centred at (gu) : 90.83720 91.03517 88.77406 assigned negative charge : -290.2263 centred at (gu) : 90.84995 91.38112 88.31494 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 53253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17575 grid for indexing accessible points = 1.400000 m= 18208 mr = 36345 m= 2226 mr = 13499 m= 67 mr = 1315 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1133 time to turn everything in is 0.4200000 number of dielectric boundary points 22586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14343 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) : 0.6086094 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3906987E-03 1.0171237E-02 midg,1,midg; midg,igrid,midg 5.4810150E-03 -5.1570330E-03 1,midg,midg; igrid,midg,midg 3.2321110E-02 3.0697482E-02 gauss-seidel spectral radius is 0.9984394 estimated iterations to convergence 201 setup time was (sec) 0.6900000 now iterating at: 14:22:51 rms-change max change #iterations 3.351862 165.1739 at 10iterations 1.485006 58.42737 at 20iterations 0.6575007 24.41303 at 30iterations 0.2925011 10.30883 at 40iterations 0.1300581 4.705024 at 50iterations 5.7839680E-02 2.222824 at 60iterations 2.5545491E-02 0.9272003 at 70iterations 1.1382942E-02 0.4232426 at 80iterations 5.0362018E-03 0.1844896 at 90iterations 2.2515215E-03 7.9499245E-02 at 100iterations 9.9749258E-04 3.7322998E-02 at 110iterations 4.4222429E-04 1.7645836E-02 at 120iterations finished qdiffx linear iterations at : 14:23:03 total time elapsed so far: 12.55000 # loops : 120 mean,max change (kT/e) : 4.4222429E-04 1.7645836E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 14:23:06 12.726u 0.465s 0:16.92 77.8% 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 21 2011 at 14:23:07 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.738742 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): -8.894000 49.60000 ymin,ymax (A): -19.29000 19.93000 zmin,zma (A): -7.871000 34.70700 x,y,z range (A): 58.49400 39.22000 42.57800 scale (grids/A): 2.738742 object centre (A): 20.35300 0.3200006 13.41800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 292.2260 centred at (gu) : 91.25587 91.55270 88.16119 assigned negative charge : -290.2263 centred at (gu) : 91.27489 92.07166 87.47253 start vw surface at 0.1100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 123189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17575 grid for indexing accessible points = 1.400000 m= 60516 mr = 88056 m= 19877 mr = 49757 m= 3727 mr = 15999 m= 328 mr = 2709 m= 7 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 3746 time to turn everything in is 1.170000 number of dielectric boundary points 50953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 14655 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) : 1.825828 object centre at (A) : 20.35300 0.3200006 13.41800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4896505E-02 8.8229097E-02 midg,1,midg; midg,igrid,midg 3.6054417E-02 -4.8031878E-02 1,midg,midg; igrid,midg,midg 0.3615852 0.3352527 gauss-seidel spectral radius is 0.9991875 estimated iterations to convergence 277 setup time was (sec) 1.610000 now iterating at: 14:23:09 rms-change max change #iterations 8.019999 343.6557 at 10iterations 4.536231 119.4731 at 20iterations 2.552787 57.77281 at 30iterations 1.425905 31.30626 at 40iterations 0.7985156 18.43070 at 50iterations 0.4452233 10.26709 at 60iterations 0.2486148 5.298378 at 70iterations 0.1386916 3.177745 at 80iterations 7.7588178E-02 1.721695 at 90iterations 4.3268178E-02 0.9236774 at 100iterations 2.4071136E-02 0.5313978 at 110iterations 1.3459780E-02 0.2817645 at 120iterations 7.5002909E-03 0.1537910 at 130iterations 4.1906126E-03 8.6988807E-02 at 140iterations 2.3419517E-03 4.8591375E-02 at 150iterations 1.3035261E-03 2.8434753E-02 at 160iterations 7.2614022E-04 1.8264320E-02 at 170iterations 4.0520629E-04 8.7547302E-03 at 180iterations finished qdiffx linear iterations at : 14:23:29 total time elapsed so far: 21.26000 # loops : 180 mean,max change (kT/e) : 4.0520629E-04 8.7547302E-03 energy calculations done at 21.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.43000 DelPhi exited at 14:23:30 21.438u 0.775s 0:23.01 96.4% 0+0k 0+0io 0pf+0w