Wed Dec 21 14:22:39 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 14:22:42 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 0.6402302 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): -3.970000 34.72300 ymin,ymax (A): -3.623000 47.92300 zmin,zma (A): -24.43500 31.17000 x,y,z range (A): 38.69300 51.54600 55.60500 scale (grids/A): 0.6402302 object centre (A): 15.37650 22.15000 3.367500 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 288.3041 centred at (gu) : 90.35846 92.69264 90.07517 assigned negative charge : -287.2643 centred at (gu) : 90.43885 92.86781 90.04337 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5495 nv = 96 ne = 84 npr = 40243 no. pairs analyzed = 40243 no. exposed pairs = 2455 no. arc points = 17233 no. surface atoms = 835 nbur = 1118 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 281 mr = 3108 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2600000 number of dielectric boundary points 2637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1712 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2080020E-10 4.8159765E-09 midg,1,midg; midg,igrid,midg 9.4587582E-09 -2.4381258E-08 1,midg,midg; igrid,midg,midg 8.2104412E-09 -5.3794209E-09 gauss-seidel spectral radius is 0.9873034 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 14:22:43 rms-change max change #iterations 0.1266332 23.52385 at 10iterations 1.2556320E-02 1.976105 at 20iterations 1.2561806E-03 0.2250361 at 30iterations 1.1989493E-04 1.9800186E-02 at 40iterations 1.2039890E-05 2.0751953E-03 at 50iterations finished qdiffx linear iterations at : 14:22:50 total time elapsed so far: 7.620000 # loops : 50 mean,max change (kT/e) : 1.2039890E-05 2.0751953E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 14:22:59 7.801u 0.477s 0:17.49 47.2% 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 Wed Dec 21 2011 at 14:23:00 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 1.920691 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): -3.970000 34.72300 ymin,ymax (A): -3.623000 47.92300 zmin,zma (A): -24.43500 31.17000 x,y,z range (A): 38.69300 51.54600 55.60500 scale (grids/A): 1.920691 object centre (A): 15.37650 22.15000 3.367500 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 288.3041 centred at (gu) : 91.07554 98.07807 90.22562 assigned negative charge : -287.2643 centred at (gu) : 91.31681 98.60368 90.13030 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 22096 mr = 40972 m= 3411 mr = 16911 m= 179 mr = 2284 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2076 time to turn everything in is 0.5300000 number of dielectric boundary points 24472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14383 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) : 0.6402302 object centre at (A) : 15.37650 22.15000 3.367500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2080548E-02 6.9834706E-03 midg,1,midg; midg,igrid,midg 3.1660825E-02 -1.8156849E-02 1,midg,midg; igrid,midg,midg 4.9575968E-03 -5.4524713E-03 gauss-seidel spectral radius is 0.9985781 estimated iterations to convergence 210 setup time was (sec) 1.000000 now iterating at: 14:23:02 rms-change max change #iterations 3.650274 155.6257 at 10iterations 1.682090 57.71920 at 20iterations 0.7765109 27.82376 at 30iterations 0.3604975 13.18286 at 40iterations 0.1649548 5.903482 at 50iterations 7.6142944E-02 2.802204 at 60iterations 3.5017230E-02 1.243380 at 70iterations 1.6215947E-02 0.6120453 at 80iterations 7.4482434E-03 0.2653656 at 90iterations 3.4414970E-03 0.1421452 at 100iterations 1.5896669E-03 5.7080269E-02 at 110iterations 7.3189248E-04 2.5493622E-02 at 120iterations finished qdiffx linear iterations at : 14:23:20 total time elapsed so far: 19.31000 # loops : 120 mean,max change (kT/e) : 7.3189248E-04 2.5493622E-02 energy calculations done at 19.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.48000 DelPhi exited at 14:23:22 19.480u 0.657s 0:22.14 90.9% 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 14:23:24 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ARG 41 has a net charge of 0.0400 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: 2.881036 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): -3.970000 34.72300 ymin,ymax (A): -3.623000 47.92300 zmin,zma (A): -24.43500 31.17000 x,y,z range (A): 38.69300 51.54600 55.60500 scale (grids/A): 2.881036 object centre (A): 15.37650 22.15000 3.367500 number of atom coordinates read : 1953 total number of charged atoms : 1821 net assigned charge : 1.040007 assigned positive charge : 288.3041 centred at (gu) : 91.61325 102.1173 90.33840 assigned negative charge : -287.2643 centred at (gu) : 91.97516 102.9055 90.19545 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 136220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 70567 mr = 98838 m= 26452 mr = 58797 m= 6138 mr = 22092 m= 745 mr = 4836 m= 40 mr = 495 m= 0 mr = 15 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 6839 time to turn everything in is 1.500000 number of dielectric boundary points 55089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 14568 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) : 1.920691 object centre at (A) : 15.37650 22.15000 3.367500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.038251 -3.2763198E-02 midg,1,midg; midg,igrid,midg 0.3285957 -0.2104837 1,midg,midg; igrid,midg,midg 2.7953751E-02 -3.4446906E-02 gauss-seidel spectral radius is 0.9992281 estimated iterations to convergence 284 setup time was (sec) 2.080000 now iterating at: 14:23:27 rms-change max change #iterations 8.609017 423.9949 at 10iterations 4.926248 125.2834 at 20iterations 2.799031 60.03831 at 30iterations 1.588657 35.70950 at 40iterations 0.9020795 18.18725 at 50iterations 0.5105782 10.60684 at 60iterations 0.2900557 6.323199 at 70iterations 0.1641113 3.666389 at 80iterations 9.2882752E-02 2.118275 at 90iterations 5.2617826E-02 1.021345 at 100iterations 2.9891562E-02 0.6134539 at 110iterations 1.6890863E-02 0.3315411 at 120iterations 9.5738126E-03 0.1888285 at 130iterations 5.4292181E-03 0.1113663 at 140iterations 3.0780623E-03 5.9837341E-02 at 150iterations 1.7388703E-03 3.4227371E-02 at 160iterations 9.8856201E-04 2.0263672E-02 at 170iterations 5.6060270E-04 1.2195587E-02 at 180iterations finished qdiffx linear iterations at : 14:23:56 total time elapsed so far: 30.64000 # loops : 180 mean,max change (kT/e) : 5.6060270E-04 1.2195587E-02 energy calculations done at 30.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.81000 DelPhi exited at 14:23:56 30.816u 0.829s 0:32.57 97.1% 0+0k 0+0io 0pf+0w